I sync Joplin between my phone and Mac using SyncThing. I set it so that on the phone it only sends and on the Mac it only receives. In this way Joplin on the phone maintains a small folder. It's been working fine until recently when I noticed large amount of data got sync'ed. So I checked the Joplin folder on the phone. It has a subfolder named ".resource" which is very large (~600MB) about the size of the folder on the Mac. Interestingly, the folder date is marked as 11/19/2020. The Mac folder also has this subfolder. I removed the one on the phone and Joplin seems to work normally, no problem with creating notes and syncing.
The .resource folder I have on Windows within my NextCloud sync directory seems to be the copy of the files in .config/joplin-desktop/resources just without the file extensions. I've only started using Joplin very recently so my assumption is that these are the files that are then copied to your local folder, hence why you can still use it all normally when you removed them. No idea what the longer term effect would be though.
!!!!! Do NOT touch any files/folders Joplin creates !!!!!!
I'm not sure why people have the need to manipulate files outside of Joplin. Do you remove a spark plug in your car's engine? Or remove the spare tire? Or remove the steering wheel (whilst driving)?
On my phone I have created only about 100 Todo notes. The phone sent them over to the Mac but not is set to receive any from the Mac. Why is there a 600MB subfolder there? So if you like the car plug metaphor, it's like I have a car worth 100000 Vietnam Dong but with a plug costing 600 million Dong. Is that normal?
I should note that the app is not designed at all to work like this. Sync state is wrong on both apps and any mistake could create a big mess. At least make sure you make regular backups.