Sadly, it deleted bookmarks during sync. Even deleted bookmarks on the SOURCE machine in a 1-way sync. The developer doesn't think that's important. Oh well.
The full story here is, floccus removes duplicate bookmarks with the same URL per folder. It is my belief that a majority of people do not intend to keep multiple instances of the same URL in the same folder. If you disagree, you may convince me over here: https://github.com/marcelklehr/floccus/issues/797
