When you removed maindb.xml did you first stop the nworks Enterprise Manager service?
If not, then your maindb configuration will have been stored in memory anyway. And Enterprise Manager service would simply write it back to the file.
You have to stop the service, delete the file, then restart the service, in order to clean your nworks config.
PLEASE NOTE - this will delete ALL of your targets (vCenter connection(s)), and return all settings to default.
You will have to add your Virtual Center server again.
Let us know if that solves the problem for you,
Vice President, Product Management