I can't make this happen consistently, but it happens enough that I cringe every time I right click on a component in the SchLib (part of an integrated lib) and select "Update schematic sheets"
I will start keeping better track of when it happens, it seems to be even innocuous things like modifying a supplier link can cause this. I think maybe whether or not I have recompiled the library affects the outcome of doing the update?
Before chasing further wanted to ask here in case I've overlooked something.
Thanks