Linux – unison-fsmonitor doesn’t detect any changes

We use a wrapper around Unison that, on failure, creates a file in /tmp based on the pathname of the directory to sync. Then, there is a service check in Nagios that checks for the presence of these files, and sends up an alert if found. This way there is the verbose Unison log for more information, a quick way to know if something went wrong, and automated email/SMS if/when it does. You could also use cron for this if something like Nagios isn't available.

I gave up on Unison. I switched to Synchronize It, which preserves modification times and is 10x faster. However, it doesn't propagate deletes both ways.

Synchronize It: http://www.grigsoft.com/wndsync.htm

Also, regarding the error

Wrong number of roots: 2 expected, but 4 provided

Look at $HOME/.unison/default.prf or %HOME%\.unison\default.prf, check if there are lines starting withroot= and remove them or move them to another profile. If there are other lines, you may review them to check if they are suitable in your case. (Apart from some far-fetched cases where one is pretty sure that they ever only synchronize one set of directory trees, default.prf should only contain options, not root specifications.)

That said, you may create and use profiles (.prf files in .unison directory) that specify directory tree roots to synchronize. Any profile may include others and even include default. The latter case comes handy to share a set of options that you want applied to all your profiles and even when unison is launched without specifying a profile on command line. For details see Unison documentation - Profiles.