As I understand it, at the end of a Muto spell the mutated objects turns back. Short term, this is simple. There are many ring duration tricks which use this. Turn a huge bonfire in to wine and pour in a goblet, there's some serious indigestion. I accept poison is easier and doesn't end with dinner guests covered in the unfortunate wine drinker. Whatever works for your magi, I don't judge.
My question is long term. The question is best asked by using an example.
A bovinomancer turns a rat in to a cow for moon as they need milk. Is the milk sustaining? In a months time the milk drinkers clearly would have metabolised the milk. Arguably there is nothing to muto back. I would argue nothing happens.
If we say the material does muto back, it opens a bunch of opportunities.
I present the spell.
Bovine fodder of the slow burn. (Muto Herbam, ignem requisite)
Transform a bonfire in to hay for moon duration.
You gift a large amount of hay to a troublesome lord. By the end of the month all the hay which is now in the form of cow waste erupts in to a huge volume of fires.
If we got a rat turned in to a cow pregnant, and each moon recast the spell so the rat stayed a cow, would they give birth to a cow?
For those who would mock the Bovinomancer, I present some spells for someone with a minor focus in cows.
The milk of human anger - Creo Aquam
Milk is created in the targets mouth for duration ring, causing them to suffocate.
The stampede - Creo Animal
A stampede of cows is created trampling all in their path. +15 damage every turn for as long as caster concentrates.
The milkmaids concern - Rego Mentem
The target considers the chosen person as important as one of the lords important creature, such as a prize bull.
If you turn a rat into a cow or even just moon duration create a cow the magically extant cow turns grass into milk as a natural process, so the milk is not considered magical. This is covered in RAW.
To be honest, if you like to eat, being able to create unlimited food that tastes good yet doesn't nourish beyond Sun can actually be a pretty cool effect knowing the sun usually sets after dinner time.
A rat turned into a cow and then impregnated would give birth to a regular calf, I suppose. I'd rule this way.
A pregnant rat turned into a cow, now that has a few corner cases. If you can target both the fetus and the rat as an individual I'd say both are transformed, and you'd have both turning back at the end of the spell. If only the rat can be targeted, I'd say you have a miscarriage (unless you are casting it as T: Group).
For turning a bonfire into hay. If you create food it disappears when the duration ends, leaving the person hungry. A magical horse fed on mundane food leaves behind a corpse. The process of absorbing food into your body seems to work fine under hermetic magic. Thus, fire turned into hay would turn back... but would the cow really erupt into flames? How much hay is still on it's body, how much became manure? Won't the fire just extinguish itself due to lack of oxygen, at most causing some increase in the cow's temperature (maybe some wounds)?
But I can see this being the cause for spontaneous combustion if the fire is strong enough. The kind of thing a Tytalus or a prankster Flambeau would do, no doubt.
Consider that a male using Persona cannot get pregnant, and that this is a more complete change than the rat turned into a cow via MuAn.
As for the new case of a pregnant rat, there are rules in HoH:MC for shapeshifting while pregnant. Again, though, Heartbeast is a more complete change than using MuAn.
This is why I went for moon duration in my example. I would think there would be no to little hay left after one month. All the hay is either cow pat or small bits of rotted hay. I think if food products are metabolised it should matter, which is why I gave an example of the kind of shenanigans one can do if metabolising things doesn't matter.
This does ask some questions about long term creo. Month duration creo food, when it disappears, what disappears? Some muscle, some fat? What body part withers if one ate just one roast chicken? Should any body part slightly diminish, or does long term creo food sustain if it's already fully metabolised?
RAW states "Conversely, magically created food only nourishes for as long as the duration lasts". I would consider if the duration is long enough that the food is no longer providing nourishment, then the magically created foot stops creating the zero nourishment it is creating when the spell duration ends.
If the magi ate a month long duration steak or three, and that's the only magical thing he ate, I would just say he's slightly thinner in the morning and leave it at that. If it's a habit of depending on magically created food, there may be more health side effects which could lead up to death if the magi ate only magical moon duration food for the last moon.
Realistically magically created food isn't regular food- its existence is magical, not natural- magically muto'd food is in the same book where its form is being held in pace magically. A steak which has a magical essential nature of being a steak due to spell craft of either type does not become integrated into the body. It obviously could be cut, chewed and broken down, and will sustain life for as long as the magic holds those properties to it, but it does not truly integrate into the body.
As to pregnant rats, ancient magic indicates that a fetus using standard hermetic magic is targeted as part, and can only be targeted as individual with the virtue of fertility magic.
In my eyes, if the Steak can sustain life while the magic holds, a poison can hinder / suppress life while the magic holds.
So according to that interpretation, the poison would kill, if it does so during the spell duration, but the symptoms would suddenly disappear when it runs out.
Which feels very much in line with how I, personally, envision enchantments, curses, magical diseases and poisons to work.
I would consider if the duration is long enough that the food is no longer providing nourishment, then the magically created foot stops creating the zero nourishment it is creating when the spell duration ends.