After restoring some old geodatabases to my new configuration, 10.3.1 on Windows Server 2012 R2 64, SQL Server 2012, a couple months ago, I noticed that the database properties were still set to version 9.3.1. I went through ArcCatalog>Update geodatabase to bring them up to the current version. Except one wouldn't update. Says it can't update because there is another open connection. I had two different connections in ArcCatalog, trying a connection as administrator and one as a user. But closing the other connection didn't fix it, deleting the other connection didn't fix it. When I look at the geodatabase properties > connections I see two connections, both from local host, but one at 6:30 today, way too early to be my current ArcCatalog connection. One is in italics, one is in non-italics. What does that indicate? When I clicked on the italics one, disconnect was not allowed, and when I clicked on the non-italics one and tried to disconnect I got "Entry for SDE instance not found in services file". What would you do here? What documentation should I be looking at?
Maybe a AGS service is accessing it? Can you shut down the ArcGIs Server...or if production, turn on service off at a time, if needed?
Or, you can run a script to see what all the .mxd's for the services are using. My guess is one of the services is still holding on to the older connection.
Italics indicates your own Connection,....the one you used to connect and open the Geodatabase Administrator window.
The other error is a known issue....as you cannot disconnect users from a 9.3.1 SDE geodatabase using the 'Geodatabase Administrator' window...
You can try the below:
1. Use SDE Command line tools to disconnect that connection
2. remove that Orphaned Connection from the 'Process Information' table from the SQL Server Management Studio
Where are the docs for the SDE command line? All that I have been able to find are the ArcServer Command line Utilities http://server.arcgis.com/en/server/10.3/administer/windows/arcgis-server-command-line-utilities.htm but it nice to know I can run these.
Just remove that Orphaned entry from Process_information table using SQL Server Management Studio...should be quicker...
Make sure you have a db backup before doing it.