I am a huge fan of Joplin but sync has become an issue for me after I switched to a new phone. My total JEX size is 430Mb. I sync via webdav and I documented some of the issues I had here:
Today I decided to re-try getting sync over webdav working on my laptop. I retired my old webdav server and started with a new fresh webdav on my Nextcloud instance. I created an empty folder and set up the webdav endpoint in Joplin settings. I clicked "sync" and immediately it says: "remote deleted" with the number going up and up. What could it possibly be deleting on the remote when it's a completely empty folder? Shouldn't it be creating files on the remote not deleting them? Is it deleting other files from my server? I checked on the server and there are various lockfiles and info.json created there. I looked at the client log and I saw something about "local deleted" so I immediately stopped it.
Even if this is expected behavior it's really badly communicated. People's data is important to them and having the first initial sync to a webdav remote start deleting files completely eliminates any confidence I had in Joplin, especially after the experiences I had trying to get it to sync to my phone, with duplicate files created after I import the JEX.
I'm at a loss now because I really like the Joplin interface and I don't want to switch to a proprietary solution like Obsidian, but I no longer have confidence that Joplin is taking care of my data. It's a bit frustrating.