I have been changing my syncing/backup methods lately, just trying them out. Every time I change the sync method on my Windows device, and I want to sync it to my android device as clean sync, it just deletes everything. I feel like this issue can easily be resolved if you just let people choose what kind of sync you need the first time you sync or choosing sync method when you change your sync option.
p.s. Having trash can feature would also be nice so if the Joplin program deletes notes accidently, you could still retrieve them manually