Windows – Removing old DC from AD, remove “subtree”

The "not working the way they were designed" thing is a generic warning that occurs when you drag and drop in ADU&C, it's nothing to do with WSUS. You can avoid it by right-clicking and selecting "Move". I've never seen any negative impact from it anyway.

As others have said, just hunting down those WSUS policies and dealing with them in your preferred manner is the way to go. If I was you though I'd build a new WSUS box and point them at it instead.

You can use dsquery (technet link) to locate inactive computers:

dsquery computer -inactive 10 -limit 0

Shows computers that have been inactive for 10 weeks or more.

From dsquery computer /? (technet link)

...
-inactive <NumWeeks>        Finds computers that have been inactive (stale)
                            for at least <NumWeeks> number of weeks.
...

You can pipe the output into dsrm (technet link) if you want to remove the listing from the domain. Please note this will not bother prompting you so apply the appropriate amount of caution.

dsquery computer -inactive 10 -limit 0 | dsrm -noprompt