It's been a while since I worked on this, but if I recall correctly...here's an example: Some Windows apps save by (1) writing a new file, (2) deleting the old file, (3) renaming new to old. The idea is that if it dies in the middle, you don't end up with no complete files. This sequence of events is actually recognized in the Windows filesystem code (if it happens quickly enough) and turned into a file-replace operation, which has very different semantics, particularly the effect of copying the metadata (think extended attributes) from old to new.

Actually the whole question of what to do with "advanced" filesystem semantics (like extended attributes) is pretty hard, especially if you're trying to sync across platforms where those semantics differ. You could just ignore them, but then if an app actually uses them (and why else would they exist?) then the file won't round-trip through the sync platform.