I've had this happen to me twice over the last month that 2FA stopped working seemingly overnight.
Now there's a service in freeipa dedicated to handling otp requests which is called 'ipa-otpd' and if that service is stopped, 2fa will not work on the ipa-server and all servers that authenticate against this particular server. 
Keep in mind that even using '_srv_' in the sssd.conf will not prevent this as the server is still perfectly responding towards requests, it just won't work with 2fa.
You can check if that's the case by checking the status of all ipa services
 [archy@ipa01 ~]$ sudo ipactl status  
 Directory Service: RUNNING  
 krb5kdc Service: RUNNING  
 kadmin Service: RUNNING  
 named Service: RUNNING  
 httpd Service: RUNNING  
 ipa-custodia Service: RUNNING  
 pki-tomcatd Service: RUNNING  
 ipa-otpd Service: STOPPED  
 ipa-dnskeysyncd Service: RUNNING  
 ipa: INFO: The ipactl command was successful  
If the ipa-otpd service is stopped like in the example above, you can restart the ipa services by using these commands:
 [archy@ipa01 ~]$ sudo ipactl stop; sleep 30; sudo ipactl start 
If that doesn't work, you will probably have to reboot the server:
 [archy@ipa01 ~]$ sudo systemctl reboot  
Also note that there's a bugzilla ongoing: BZ 1953554
You might want to check the logs for any reason why this service crashed. In my case the logs were empty and 'journalctl -u ipa-otpd.socket' did not return any useful information though.
Feel free to comment and / or suggest a topic.
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