I did a test (my first one) of patching 3rd party software for notepad++ using Configuration Manager.  I did a straightforward one and it worked great!  Strange that it doesn't leave a status in the local Software Center that it did the update though.

So I thought I'd test the number one thing that would come up and that's, "what if a user has it running at the time the patch was applied".  Then the problem revealed itself, all the other files in the program directory updated, except the executable.  On the SCCM side, complete success.  Even when I stopped and restarted the program I didn't even get the nag from the software itself that it had an update but still was running the older version.  So even the system thought it had updated and any subsequent attempt through SCCM could not force it to "reapply". 

Only when from in the program I forced it to check for an update was I able to repair the failed update. 

Does this patch not actually check to see if it's running while trying to perform the update?