This might seem silly, but it is literally as simple and going to Add/Remove Programs and uninstalling the Console and reinstalling it (Framework, then followed by Full Disk, Helpdesk, Removeable Storage, etc, as required).

Most of the configuration data is in the database, and the policy configuration is held in the GPO.  None of this stuff is in console itself.  As long as the Database and the management server itself are not touched, you're fine.

Regarding your issues however, it sounds to me like you've had to update the password on the IIS Check in account, and that some clients are locking it out by using the old password, is that right?

Just to clarify, the process for changing the password on this account is:

• update creds in AD
• update creds in SEEMS Configuration Manager
• create and export new Framework Client package with updated creds from the SEE Console
• perform upgrade install on all existing clients with new Framework Client package

It is important to note that the creds used for checking in cannot be udpated by policy, and can only be done via a client upgrade:

http://www.symantec.com/docs/TECH122714

That was a complete answer, thx. 

2012-12-13 00:04:18 10.130.0.96 POST /GECommunicationWS.asmx - 1080 Domainx\userx 10.130.9.5 Mozilla/4.0+(compatible;+MSIE+6.0;+MS+Web+Services+Client+Protocol+2.0.50727.5466) 401 1 1326 31

Any ideas how to remove this user from whatever it is?