I needed to sync a few times today as I'm working on a plugin. After one of these syncs my favorites folder was mostly deleted and many nodes on home page went missing too. I restored a backup and sync'd again and things are OK now.

In this thread: https://forum.universal-devices.com/topic/46514-ud-mobile-stopped-working-with-1-of-2-isy-after-sync/

You told me to switch to legacy sync mode. Is there any reason for me to continue using legacy?

There should be no reason to be in legacy mode unless something is not synchronizing. But I think all of these issue are resolved (the new method is the same method used by eisy-ui)