Syncing issues between Mac OS and Ubuntu, some files went missing then reappeared

Hello,
I've had dropbox beta for years, and I have the desktop app on two computers: one on mac os, the other on ubuntu.

My ubuntu computer had a problem, I had to reinstall it, and as a result my synchronised files were overwritten. When I turned the computer back on with the new distribution, and started the new drobox desktop, it apparently reinstalled all the folders that were on the cloud. But when I opened a Books folder with 1600 files, I realised that they had all disappeared, everywhere: on the cloud, on the mac, on the ubuntu.

I tried to recover them from the cloud, since only two days had passed, but there was nothing there. I then bought the pro version, and suddenly the Books folder reappeared, without me even starting a recovery, and the files resynchronised on both computers.

Why all this? I can't quite figure it out. On the other hand, I've since noticed that something has changed (I don't know how long ago, not for long): before, if I threw a file on my computer, a window would ask me if I wanted to keep the original on the dropbox cloud. Now that window doesn't appear, and if I throw a file away, it also disappears from my cloud. (And if that's why the Books folder disappeared, because when I restarted ubuntu it was no longer on the computer, then all the other folders should have been emptied, which wasn't the case).
Does anyone know how to restore this function?

thanks in advance