Extremely frequent diff based backups? Firejails?
The latter seems a more appropriate/thorough solution, but isn't that convenient, seems mostly people use it for select programs they already slightly distrust.
I have only lost data due to hard drive failure, or at my own request (i.e formatting over what I thought I had backed up).
I recently enabled TRIM on my full-disk-encrypted SSD system. No sign of data loss yet.
I have always used ext3/ext4.
My personal preference is to rsync to a backup host in a daily cron. Hourly for important directories. That backup host then runs rsnapshot [1] locally and the snapshots are made read-only. Important files are then backed up off-site. rsnapshot is just a perl script that creates multiple diff snapshots and uses hardlinks to save space. It is available for most distros. I believe it is also in macports and homebrew for mac.
Google Drive and OneDrive has similar solutions today but they often only takes the home folder, the one we used could take a lot more.
A lot of information about Qubes talk about protection against attacks, but it's also useful against unintentional issues, and I'd argue that's a much more common case where Qubes shines.