I encountered a problem with Obsidian Sync when using it with Metadata Menu plugin. In that plugin there is an option to add a fileclass after a creation of a file:
Unfortunatly when Obsidian Sync creates a new .md file locally this thing is triggered everytime - obviously causing annoying overlays of a fileclass selector (they add up actually).
I am not sure if that can be addressed on the Obsidian Sync side – or this has to be something the Plugin author needs to look into this. I have opened an issue here: Fileclass option conflicts with Obsidian Sync · Issue #781 · mdelobelle/metadatamenu · GitHub