I have created some test notes in joplin, with no sync set up.
I set a directory in the file system to do some sync testing, and sync writes nothing out - but instead gives me an error saying this would delete a bunch of things and is disabled by the (very wise) safety setting.
So how does one 1st time sync a pool of notes out of joplin into the sync respository for the first time?
This phrase caught my attention. Is it possible that you created a folder manually, and now Joplin thinks it is necessary to sync with its empty folder = delete everything from your local computer?
OK, when I just tried this again, letting joplin create the new directory, it did the expected thing.
BUT - when I pre-created the directory, joplin wanted to "sync with null" and the safety system kicked in.
So yes, it when switching to a pre-existing directory, even an empty one, it wants to treat this as 'sync with null' rather than fill in an empty sync repository.
[To be fair, it gives some warning. To be double fair, the export/import tools appear to actually work so making a real backup is easy.]