I found my Server 2012 WSUS folder had exploded to over 500 GB  so I followed the instructions here to fix it. Unfortunately, the WSUSContent folder is still empty apart from a file anonymouscheckfile.txt. I have tried rebooting and left it overnight.

There's nothing obvious in the event logs. The WSUS Cleanup Wizard just gets stuck on 'Deleting unused updates...'

How do I fix it?

I suppose I could just uninstall and reinstall WSUS, but I'd like to take the opportunity to

And I've just started getting errors in the event log after 'Deleting unused updates' crashed:

Log Name:      Application
Source:        Windows Server Update Services
Date:          13/08/2015 13:01:22
Event ID:      10022
Task Category: 7
Level:         Error
Keywords:      Classic
User:          N/A
Computer:      Aberdeen.qts-home.local
Description:
The last catalog synchronization attempt was unsuccessful.

Log Name:      Application
Source:        Windows Server Update Services
Date:          13/08/2015 13:01:22
Event ID:      12032
Task Category: 9
Level:         Error
Keywords:      Classic
User:          N/A
Computer:      Aberdeen.qts-home.local
Description:
The Server Synchronization Web Service is not working.

Log Name:      Application
Source:        WSusCertServer
Date:          13/08/2015 13:02:07
Event ID:      0
Task Category: None
Level:         Information
Keywords:      Classic
User:          N/A
Computer:      Aberdeen.qts-home.local
Description:
The description for Event ID 0 from source WSusCertServer cannot be found. Either the component that raises this event is not installed on your local computer or the installation is corrupted. You can install or repair the component on the local computer.

If the event originated on another computer, the display information had to be saved with the event.

The following information was included with the event: 

Service stopped

Log Name:      Application
Source:        Windows Server Update Services
Date:          13/08/2015 13:02:22
Event ID:      7032
Task Category: None
Level:         Warning
Keywords:      Classic
User:          N/A
Computer:      Aberdeen.qts-home.local
Description:
The WSUS administration console was unable to connect to the WSUS Server via the remote API. 

Verify that the Update Services service, IIS and SQL are running on the server. If the problem persists, try restarting IIS, SQL, and the Update Services Service.

System.Net.WebException -- The operation has timed out

Source
System.Web.Services

Stack Trace:
   at System.Web.Services.Protocols.WebClientProtocol.GetWebResponse(WebRequest request)
   at System.Web.Services.Protocols.HttpWebClientProtocol.GetWebResponse(WebRequest request)
   at Microsoft.UpdateServices.Internal.DatabaseAccess.ApiRemotingCompressionProxy.GetWebResponse(WebRequest webRequest)
   at System.Web.Services.Protocols.SoapHttpClientProtocol.Invoke(String methodName, Object[] parameters)
   at Microsoft.UpdateServices.Internal.ApiRemoting.ExecuteSPGetUpdateServerStatus(Int32 updateSources, Boolean includeDownstreamComputers, String updateScopeXml, String computerTargetScopeXml, String preferredCulture, Int32 publicationState, Int32 propertiesToGet)
   at Microsoft.UpdateServices.Internal.DatabaseAccess.AdminDataAccessProxy.ExecuteSPGetUpdateServerStatus(UpdateSources updateSources, Boolean includeDownstreamComputers, String updateScopeXml, String computerTargetScopeXml, String preferredCulture, ExtendedPublicationState publicationState, UpdateServerStatusPropertiesToGet propertiesToGet)
   at Microsoft.UpdateServices.Internal.BaseApi.UpdateServer.GetStatus(UpdateSources updateSources, Boolean includeDownstreamComputers, UpdateScope updatesToInclude, ComputerTargetScope computersToInclude, UpdateServerStatusPropertiesToGet propertiesToGet)
   at Microsoft.UpdateServices.Internal.BaseApi.UpdateServer.GetReplicaStatus(UpdateSources updateSources)
   at Microsoft.UpdateServices.UI.SnapIn.Common.CachedUpdateServerStatus.GetFreshObjectForCache()
   at Microsoft.UpdateServices.UI.AdminApiAccess.CachedObject.RefreshCache()
   at Microsoft.UpdateServices.UI.AdminApiAccess.CachedObject.GetFromCache()
   at Microsoft.UpdateServices.UI.SnapIn.Pages.ServerSummaryPage.backgroundWorker_DoWork(Object sender, DoWorkEventArgs e)

Log Name:      Application
Source:        Windows Server Update Services
Date:          13/08/2015 13:02:22
Event ID:      7053
Task Category: None
Level:         Error
Keywords:      Classic
User:          N/A
Computer:      Aberdeen.qts-home.local
Description:
The WSUS administration console has encountered an unexpected error. This may be a transient error; try restarting the administration console. If this error persists, 

Try removing the persisted preferences for the console by deleting the wsus file under %appdata%\Microsoft\MMC\.


System.NullReferenceException -- Object reference not set to an instance of an object.

Source
Microsoft.UpdateServices.UI.SnapIn

Stack Trace:
   at Microsoft.UpdateServices.UI.SnapIn.Pages.ServerSummaryPage.backgroundWorker_RunWorkerCompleted(Object sender, RunWorkerCompletedEventArgs e)

Hi,

It seems that the server cleanup wizard is overloading due to the large number of the unused updates.

Please check if the following article is helpful:

http://blogs.msdn.com/b/jjameson/archive/2009/03/28/wsus-server-cleanup-wizard-hangs-on-deleting-unused-updates.aspx

Normally, server cleanup wizard should be run periodically to keep the WSUS server well maintained.

Best Regards.