Brilliant, I was able to reproduce this on my side, thank you for the report.
What's happening in short is that FSEvents (
https://en.wikipedia.org/wiki/FSEvents) sends bogus paths when notifying about changes.
For instance, when changing something in
/System/Volumes/Data/Foo the system sends events for
/Foo, which doesn't even exist
No wonder Nimble Commander ignores these paths and doesn't refresh listings.
Finder also doesn't catch notification events in this case on my setup - the problem is in the system itself.
Honestly, I don't know what to do with it - I have no desire to add further hacks for this clusterfuck with firmlinks and R/O root that Apple has made.
Maybe just don't touch anything inside
/System/Volumes/Data/ at all? Clearly the system itself barely handles this set of oddities.