@Kradnam the once that was absorbed by the founder was also not recovered(the one that rena got to get a promotion that's why the golem was no longer a problem, they never appeared actually inside Isaac's shrine even though they should automatically attack anybody when someone other than than the blacksmith family enters ) so it's not exclusive to skeleton knight if it get moved it's permanently moved even that treasure chest is permanently moved across all timeline and the Lu-Lium is technically absorbed by the knight guy so what ever loop it is it's staying inside his stomach.
I guess there's a chance that she's significantly weaker in the next loop cause only half was eaten but then again the other half was deleted by the magic barrier. only way to find out what happens to her is to die what ever the result is chances are it will effect rena greatly