And here I was just trying to imagine how a SG is burned at the stake in game for ruling against the pope... unless you are suggesting players murder their SG for disagreeing with medieval papal authority...
when it comes to setting in game the pope may or may not be infallible, but the SG certainly is.
How long? 
Well, first of all I have to point out that the Reformation (and the religious wars and persecutions that followed) predate 1870 by a comfortable amount.
And secondly, I wasn't saying that the Pope felt threatened by the 1049 synod. At the worst he would have felt miffed.
But if a parish somewhere started a movement that said: "Our church is tainted by Satan and that's because the bishop who consecrated it was a simoniac sinner..." Well, Luthor and Hus and all of that lot were saying things a touch less disrespectful than that.
And my point is that theology and Dominion lore are not the same ability, and that what the church ruled does not have to be what the game mechanics follow, if the divine in your world works a bit differently...
Yep. That is why the liber gratissimus was indeed gratissimus, and despite his previous book Peter Damian became a cardinal and a major figure of the Church Reform after Leo IX.
Yes. Actually, the remainder of the worldly rule of the Pope ended a very few months after the Padre Aeternus declared him infallible.
two things I have found poking around wikipedia that connect to this-
Take a quick look at the historical development of canonization in the Western Church.
As that process changed, also the way to determine, whose relics are worthy to rest in an altar changed - but this did not affect retroactively the patrons of churches and altars, or local devotions.
The "civil authority of the Church" here describes the function of bishops as worldly lords: the possession and control of land, rights, titles and services.
Defying and rejecting this civil authority was a worldly issue, not heresy, and unlikely to affect the Dominion any more than rejecting the authority of - say - a baron. In both cases, worldly courts had to resolve the conflicts.
Also, canonization does not make someone into a saint. Canonization is merely official recognition from the church that someone already is a saint.
The point is that this inspired a point- which is to say that a church which is sanctified with false relics of whatever source (inspired by the wikipedia article) would not develop a dominion aura since the Catholic process does not independently bless the space, unlike the Muslim and Jewish consecration.
As to the civil authority the first point is this- if you are rebelling against the civil authority of the bishop, and the bishop is actively suppressing your rebellion, are you going to go to church in that Bishop's cathedral? Maybe you feel it is worth walking to the next town over, or skipping church a few weeks at a time and going to the next town over on Christmas and Easter. Rebelling against the civil authority of a bishop is likely to have a significant impact on church attendance...
Just that the wiki reference shows, that the ways to qualify relics in altars changed over time, while canon law has "Unaquaeque ecclesia suum habeat titulum qui, peracta ecclesiae dedicatione, mutari nequit": so a dedication to a saint, once performed, cannot change any more and remains valid.
If you lived in a town in the middle ages, you used that town's cathedral.
Yes, you might have skipped functions that a despised bishop held. But the cathedral belonged to the town, not to its bishop - and many canons and priests held functions there that you could attend without distraction by your wordly quarrel with the bishop.
This assumes that the church's general ruling covers all situations. YSMV, but the false relics known at the time to exist (it was said that if all the pieces of the true cross were combined you could build 200 crosses) would not be the foundation of a divine aura. It isn't fundamentally about the rules of the church, but the rules of the divine.
As to skipping functions of a despised bishop, 1) I was talking about an active rebellion, not a social disagreement, where "the town" which owns the church is also ruled by the bishop, and while the functions may or may not be safe to attend, the question is the confidence of townspeople in that safety in their decision to attend that church. My statement, if you go back to it, is that this is not beneficial to maintaining the aura, not that it would inherently collapse. YSMV, but if someone is looking for how a city might lack a divine aura this sort of conflict could certainly serve as explanation.
The Divine is always YSMV. I just can explain to you 13th century church procedure, which very much looked for consistency and practicability.
Sorry, in that case the functions were rather unsafe for the bishop. Not so much for the townspeople. In the 13th century, finally the archbishops of Cologne moved to the Godesburg and left the city and its cathedral alone.
Bishops actually ruling their towns became rare in 13th century Middle and Western Europe. Even in Germany, most towns had acquired their important rights from their bishops over time.
RoP: D is pretty clear that the Divine has allowed several copies of relics to exist, citing for example, multiple heads of John the Baptist, each of which are equally valid. So you shouldn't take a purely rational approach to the number of relics - in Mythic Europe, they are miracles, embodiment of the will of the Divine. Now, of course, there are also false relics sold by charlatans, and RoP:D is also clear about that. But I would assume there are enough clergymen in the church capable of identifying a real relic from a false one through such powers as Sense holiness and unholiness and true faith that the church wouldn't be easily deceived by charlatans peddling false relics. As such, I would place the false relics in a lot of places, but very few in a church, and none in an important church. The majority of false relics, my guess, are held by the nobility and the trading class.
I think it would depend heavily on the church. For example I found one church where the mantle of its founder was used as a holy relic for consecration- and by all accounts the founder (who was never made a canon saint) is more of a politician in divine office than a saintly character. Are you going to tell his church that his mantle doesn't cut the mustard? The church became important over centuries, but it did not start out that way, and even then its importance was more political than theological. At some point replacing such a relic becomes a problem because it involves admitting that the church has stood for centuries without being properly consecrated.
The overall point being that simply belonging to the church does not make something infallible, and that there may be cases where the impact of that is significantly greater than usual.
The other question I am left wondering (not covered in RAW) is what happens if an infernalist desecrates or removes the relics of an established dominion aura that was not also blessed, relying on the ephemeral aura to support the dominion aura?
In such a case - which you made sure not to refer too precisely - the "Unaquaeque ecclesia suum habeat titulum qui, peracta ecclesiae dedicatione, mutari nequit" would prevent official doubt in the Church. For local concerns, the founder was a saint - and it would not matter (see above) that there was no formal recognition by a pope.
If you decide for your saga, that this specific local saint was not enough to cause a Dominion Aura in that church, play it that way.
See RoP:TD p.44f:
As objects of great power and value, relics are periodically translated, stolen, sold, traded, or otherwise moved from one location to another. In cases where a theft or other illegal acquisition has occurred, if the effort is successful it is often assumed that the saint inspired the criminal, with the success indicating that the saint wanted the relics to be moved, and so attempts are not always made to recover them.
In the case of attempted theft and desecration of a relic, the saint may also cause a miracle. A SG can take a choice of RoP:TD p.88f Saints' Miracles (from Flabbergast the Impertinent to Swallowed Alive and Sent to Hell), or find inspiration from the many legends of attempted and failed robberies in church. A creative SG will find a miracle matching the saint's personality and confirming her legend.
If the relics were stolen (or desecrated) what would be the effect on the aura though- furthermore what would be the effect on the church's perception of the aura. If false relics are stolen would the church inter new relics and re-consecrate the church?
I assume that if a relic is desecrated that is unlikely to be acknowledged by the church, and as you note is inversely likely compared to the power of the saint involved... at least under most circumstances. (hypothetically a saint might allow their relic to be desecrated under very unusual circumstances, probably relating to the behavior of the congregation on an epically bad scale- did I include enough qualifiers in that?)
Provided that:
(1) the Dominion Aura depended on the masses in a single church,
(2) that church had a single consecrated altar,
(3) the patron saint of that altar for unknown reasons does not resist the desecration of that altar,
(4) that altar actually gets desecrated,
then that place ceases to be a site of worship.
RoP:TD p.12 has then:
If a place ceases to be a site of worship, the Dominion starts to fade. In general, the time it takes to fade is the same as the time for which the place was a site of regular worship.
Provided that the Church has not given up the area, it hence has time to remedy the desecration by reestablishing a place of worship there. There are many obvious ways to do so before the Dominion Aura vanishes.
Why? A desecrated relic would of course be replaced, as would a desecrated altar or church, if the Church is still interested in the area.
because acknowledging the desecration is admitting that the forces of satan got the upper hand. In many cases they may not be able or willing to admit that to themselves (especially if the effects are as subtle as you suggest). The church is overseen by humans after all, and human capacity for denial is pretty high.
Once. There is no shame in acknowledging that. There is a lot in not remedying, though.
Anyway, there might be some penance done by those charged with the care of the relic/altar/church.