Regarding the "deleting remote items" on initial sync, see this comment. Likely nothing to worry about, and just poor messaging from the application: Unexplained Deleted Files - #2 by personalizedrefriger?
It did the same thing when I recently sync'd for the first time, and it definitely didn't delete any of my notes.
This messaging may be improved in a future version: Desktop,Mobile,Cli: Include types of synced items in the sync status message by personalizedrefrigerator · Pull Request #11488 · laurent22/joplin · GitHub