Keeping WSUS working well can be a bit be more involved than Microsoft would have you think. If you are finding you are getting “timeout” issues on your WSUS cleanup wizard, then you may need to resort to some back-end WSUS database cleaning.

The link below is not quite a blow by blow set of instructions, but it is close and should be enough for most IT Admins to understand. My hint would be to remember that you need to run Microsoft SQL Server Management Studio with administrator rights.

I found that deleting a few of the topmost updates listed after the query; along with increasing the timeout setting to 0 (aka no timeout); was enough to get the WSUS cleanup moving once more.

Running the table query to list the number of updates found whilst the wizard is running is a good way to check if progress is being made.(Sometimes the WSUS Wizard progress bar can take a while to reflect progress – especially if there are a large number of updates to be cleaned/removed).

https://social.technet.microsoft.com/Forums/office/en-US/7b12f8b2-d0e6-4f63-a98a-019356183c29/getting-past-wsus-cleanup-wizard-time-out-removing-unnecessary-updates?forum=winserverwsus

Good luck.