Well, I know for a fact that missing normal maps ("..._n.dds") can also cause the rigging to get lost, for whatever reason that might be, but it is... though you said it was working fine before but now it isn't anymore, so definitely "something" must have changed.
This scenario with replacement textures randomly getting lost over time strangely reminds me of those times of old, where people were still using antiquated Archive Invalidation techniques like just entering the texture files into the list in "Archive Invalidation.txt". You working with "re-textures" means you know of the need for Archive Invalidation, or your replacements would not work at all.
This method of old was done away with for exactly that reason, for at some point, some random threshold, some files from the list were ignored and the game was either falling back to Vanilla or acting as if the files would be missing instead. Until at some other point, once you added or removed a couple more entries from said list, certain files started working again and others failed... everything pretty much random in fact.
But this surely can't be it, can it? You're not using this antiquated means for your Archive Invalidation still, or are you?
edit: That said, is it "only" in the CK or also in the game?