When that happened, had the long initial sync already completed or barely started?
I assume it had completed. Use a new profile on your JD, repeat the same thing you did, and when you see all your notes after initial sync completed, immediately export all notes as JEX. Now you have a single file backup of your data and you can breathe a little. Next, use a new profile again on your JD, don't setup sync, simply import your JEX. Are all your notes there?
Note: to get a good view of your data size and number of notes, use help > sync status in your JD at any time. Here is mine below as an example.
