Funny, it's 4 years later and my opinion is still the same (ref DutchForce thread).

The second (Grundig) link sounds good, but, in addition I would suspect mismatches with component links (open PCB file -- Project/Component Links). As far as I know, forwards and backwards annotation should always give the correct results, including renaming component designators. Because they are supposed to be matched by UID, rather than designator. If those aren't matched correctly, then you'll get the shit being fucked up with.
I've seen the same problem, from time to time, in Multisim/Ultiboard; I don't know how they keep those things straight, if there's a hidden UID or if it painstakingly tracks manual changes, or matches parts by netlist, or what. Sometimes you can rename components and the ECO will be simple, other times it says, "oh shit no son, you done fucked everything up, delete that old shit here's some replacements".
I imagine other tools (KiCAD, Eagle, Diptrace,

) have similar problems. Seems like one of those things that either has no reasonable solution, or that never ever gets programmed right, from the start.
Tim