The ‘Unable to find site id’ error is just a warning, quite never is a problem or be the root cause of an issue.
Check if with the Relay Diagnostics is possible connect with the server and the server is responsive.
Try login using a local and not a remote operator. Check if using the console installed on the same machine than the server change something. Double check for firewalls in case of remote console. Try if something change restarting the server service. Check if stopping everything else rather then the server service it is possible login.
If it is possible login with a local master operator, check the Health Check Dashboard for any problem and fix them.
Check there are no too many agents directly connected to the server and/or not too many actions opened.
Cleanup the server using the BES Computer Remover and BES Audit Trail Cleaner cleanup tools …
If none of these actions can help, could be an idea open a case and involve the Bigfix support team