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
myhost.mynetwork_mydatabase
You could try stopping the dbconsole with
set ORACLE_SID=mydatabase
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
Remove HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\OracleDBConsole[SID]
2. Remove the existing setup from the filesystem
Delete %ORACLE_HOME%\DomainName_SID
Delete %ORACLE_HOME%\oc4j\j2ee\OC4J_DBConsole_DomainName_SID
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