fsNotifier chokes on some code bases that link onto themselves because it uses inotify watch descriptors as file system node indices. These are unique per inode but sometimes inodes are linked or moved. This is a table collision (the watch descriptors match but the paths don't) and so fsNotifier bails out. If it bails out too often, IntelliJ stops watching the file system.
On the codebase I work with, this was exclusively happening to my project directories when npm was downloading to .staging directories and re-linking after. Our process refreshes certain modules on every build, so a few builds quickly stopped IntelliJ from watching the file system.
My hacky fix is to ignore paths that contains .staging: https://github.com/nuzayets/intellij-fsNotifier-hack/blob/master/inotify.c#L236
Use like this:
./make.sh
sudo mv fsnotifier64 /opt/JetBrains/idea-IU-211.7142.45/bin/fsnotifier64