When plugins run against a linked part, their edits typically unlink things that are unlinkable. This is the only way that plugins have of unlinking, since the linkage data itself is (as far as I can tell) invisible to them. However two items that manually unlink but do not plugin unlink are tie alterations and measure number positioning (and hide/show) adjustments. I recently found myself stupidly clicking on bar after bar in a linked part and randomly dragging the tie to unlink it. Just so I could then run my plugin to make them look right without affecting the score. (C Score, transposing part.) It took me right back to the Finale experience of the 90s.
I previously sent this privately to Michael Good, since he is the plugin developers' contact. I sent him technical details of exactly which internal structures I'm talking about. If they are of value here, I can attach them. But I thought I would at least mention it here so it will be in the database.