While editing the B part of Romanza, I inserted a key change to E major and told it to apply it to all segments at this time. I had linked copies of the master segments I was working on, and all the linked copies got weirdly corrupted after performing this operation. Quarter notes became double dotted 8th notes, bar lines turned red everywhere, and the notation that was supposed to be on the track that would be exported was all screwed up, or at least its display was corrupted. I didn't try to export it to LilyPond like that. I just wiped out the linked segments and will take new copies. The masters are fine.
This needs proper investigation. Part of the key might be importing a file full of triplets that Rosegarden doesn't handle properly, which leaves everything in a slightly funky state even after you go fix it all manually as best you can. I say this because even after de-tupleting all the non-tuplets and manually fixing all the triplets, every so often I'm getting spurious 16th rests that spring into existence and have to be normalized away, repeatedly.
All that is well and good, just this file is too close to being finished to start using it as a guinea pig. I'll go back to the original MIDI or something when I get a chance to look into this for real.
It may turn out I can't repeat it, or I'm mistaken about how I arrived here. Anyway, better to mention it and shoot it down later than to ignore it.