Unfortunately it's not possible to know what the issue is from the info provided. In many cases, mysterious issues like these are due to fiddling with the sync target, changing the config, or trying to fix something on the server and accidentally breaking something else.
More rarely it can be a bug in the WebDAV server (Nextcloud for example has a bug that can cause users to lose all their local Joplin data - bug that's now mitigated by the fail-safe I've added in Joplin). Every time I investigate in depth these sync issues it always end up being something unrelated to the app itself and as of now there's no known bug on the sync algorithm itself.
In your case I'd suggest to use the app as normal, but backup the data from time to time. There are also examples of crons on the forum on how to do this automatically - for example: Best method to backup notes - #2 by laurent