Data loss on uploading an Sqlite file

One guess: you copied a sqlite file that was still in use by some other process, and not all the data was in the main sqlite file. (See https://www.sqlite.org/tempfiles.html for other files that may be involved).

As a next step, I'd suggest you check and log the size of the sqlite file right before uploading to Dropbox. Then check the size of the file that was uploaded. If they're the same, then you know the issue doesn't relate to Dropbox and is instead about the fact that the file you're uploading isn't what you expect.