This all makes me grateful that I use sqlite3 instead of FS for storage, even for fairly trivial projects.

Could you expand a little on how you're doing that?

I've been thinking about transitioning entirely to sqlite for all my data.

The GP may seem like sarcasm to some ... sqlite is an overlooked, novel, and faster way (up to 35%!) to store things than the filesystem [0].

You can use something like libsqlfs [1] for POSIX file heuristics with sqlite as the backing store.

One HA single primary/multi-master solution to use sqlite may be drbd.