I love the idea of this plugin, but - yes - there should be a big caveat here regarding this - I also had the same issue, wondering why suddenly hundreds of notes were needing to be updated during sync, and why the updated dates (critical meta-data for me) were being scrambled.
Originally I had assumed that the plugin was modifying tags and that this caused the issue, but I note that if I manually change the tags on a note, it doesn't update the sort order in the note list (when sorting by "Updated date"). Some clarification would be great before I dare to try it again...