And now allmon3 (which was working) throws up the error “allmon3 is not responding to requests for this node”. The passwords are correct, I've obviously broken something to stop it talking with AMI.
Any ideas if this can be fixed without a complete fresh install?
The asl3-update-nodelist and Allmon3 are entirely unrelated. Allmon3 does not use the database file provided by asl3-update-nodelist. Other than the fact that there's never a reason to run asl3-update-nodelist manually, it wouldn't have impacted Allmon3 in any way. Did you try restarting the service and looking for errors in the log?