Does anyone have a real handle on what happens when you load up a mod in the SE CK for the first time?

I know that the meshes are converted to a new version of nif, using BSDynamicTriShapes in place of the older TriShape/TriShapeData combo. This has given me problems for a character with a custom head mesh that didn't convert properly.

Texture sets now reference more maps, and some extras may get generated (or copied from a built-in template?). I have problems where an NPC gets a white tint mask generated, and the CK doesn't want to let me edit it. This affects only the head, as the tint gets applied (apparently correctly) to the body.

The message "Textures should have been converted in batch" or similar - what is that missing process?

Are FaceGen files always updated on save, or is Ctrl+F4 still needed after a change? For that matter, will saving the esp re-break anything after it's fixed?