Looks like I was able to get back into the web gui by going into the docker image and running
OMD[cmk]:~$ cmk-update-config -vvv --debug
parsed arguments: Namespace(debug=True, verbose=3, conflict=<ConflictMode.ASK: 'ask'>)
ATTENTION
Some steps may take a long time depending on your installation.
Please be patient.
Verifying Checkmk configuration...
01/04 Rulesets...
02/04 UI extensions...
03/04 Agent based plugins...
04/04 Deprecated .mk configuration of plugins...
Done (success)
...
...
...
16/17 Update backup config...
17/17 Removing deprecated allocated_ports file...
Done (success)
OMD[cmk]:~$
After that the web GUI came back. Had to re-run some discoveries on host but eventually everything returned back to normal.