1. It seems that the only way to stop the DB Check Up is to kill the pdmserver process, which is not a very good thing to do.  Should you be forced to do this, you can read the results (so far) of the DB Check Up in the PDM log file.

2. You can read the results of the DB Check Up in the PDM log file ( <pdm_loadpoint>/text/pdmlog.txt ).  Messages in the log which are labelled 'warning' can seemingly be ignored as they will not prevent a DB Check Up from being passed.  Any other messages such as 'invalid record found' should be addressed.  For example, you can simply delete the offending revision of the object.  So it is possible to address problems that have been found in even an aborted DB Check Up.

3. The environment variable RPC_TIMEOUT can come into play if the check up query exceeds the timeout period (which I believe is 90 minutes by default).  If the timeout period is too small, the 'DB Check Up' may not receive a response from the server within the timeout period, and the client session will restart the query, resulting in an infinite loop.  Instructions for how to set this environment variable can be found on the page PDM Server Timeout.

4. The practical way to perform a full 'DB Check Up' is to set up a unix script and a pdm trail file to perform the query overnight, when nobody will be trying to use the PDM server.  You could also set up a script to check the status of the PDM server early in the morning, so that you can see whether you need to rush into work early to kill and restart the server process.  My main database is about 70GB in size and took just over half an hour to complete the check up.

5. If you receive the message "References between database objects may not be complete - Please contact PTC Customer Support for assistance" then the normal course of action is to send the database to PTC for repair.  If you do not have support for Pro/PDM (which is more likely as the product is now retired) then PTC will repair the database for a fee.  However, I believe that the tools that PTC use to repair the databases are unofficially available in the public domain, and if you can obtain them then you can attempt to repair the database yourself, but you must make sure you have a back up in case things go wrong.