I think another angle is Covenants that are clearly not Diedne, but there are no records of them having ever existed. Maybe they even have Order of Hermes Lore books that contain information unknown and preferably forgotten…
For example, in my formerly long running 1st Crusade Campaign, a big setting conceit is that the Schism was so massive that whole 14th house (Seswatha) was destroyed and no one even remembers it at all (in part due to powerful magics used).
Canonically, what the Order did after 1012 was destroy records of old covenants and Diedne sites so that they were much harder to locate. There is also canonical writings (so far as I recall) pointing out that one can bring the attention (and wrath) of Quaesitors if it comes out you’re looking up old Diedne sites. Clearly in my mind, this means many Tribunals may have old rulings, rarely brought up, that consider it a low or high crime to investigate the Diedne. So in effect, social penalty and removing evidence.
But if your PC’s are built for various types of magical investigations and archaeology, they likely could find a lot… But they will have the trouble of locating a site in the first place, and secondly, dealing with any traps in those sites. Consider that many American revolution and civil war battle sites have been properly located with modern archaeology simply by finding the bullets and canonballs in the ground using metal detectors.
You could even have them find say, a magical grove of clearly modified trees that is environmental evidence of some kind of nearby Diedne site… Perhaps they simply got missed because the covenant was taken out in Winter, and the snow covered up the magical nature of the grove… And at the time, there was too much urgency to kill Diedne magi rather than investigate the site in detail afterward.
A magical section of road, via Mercurian magic that never fall apart, could be evidence of an non-Diedne covenant, for example. Lots of environmental clues you could throw at your players.