You can find the config files for the database specific DBCONSOLE in your ORACLE_HOME under a direcory named with the FQDN of the Host, an underscore, and the SID. eg
You could try stopping the dbconsole with
emctl stop dbconsole
Then fiddling with the config files and dir names and then restarting the console.
If that doesn't work then you can reinstall the dbconsole into a database with command line tools. I'd lookup the full set of help on EMCTL.
Update: I had to recreate some DBCONSOLE repositories recently.
The following steps worked well.
Manual DBCONSOLE removal and recreation
1. Remove the existing Windows Service
2. Remove the existing setup from the filesystem
3. Remove the SYSMAN schema from the database as SYS or SYSTEM
drop user sysman cascade;
drop role MGMT_USER;
drop user MGMT_VIEW cascade;
drop public synonym MGMT_TARGET_BLACKOUTS;
drop public synonym SETEMVIEWUSERCONTEXT;
4. Run the Database Configuration Assistant
Select the database from the list
Ensure that the DBCONSOLE option and the Enterprise Manager Repository options are ticked