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It's difficult to say for sure without looking at all the other logging (namely STDeployerCore.log), but near as I can tell, the WinSCP patch you pushed likely timed out after 12 hours since it didn't return a response, and then the deployment moved onto the rest of the patches (the rest of which seem to not have had an issue). We can dig in more deeply in a support case if you'd like, but that's what it looks like to me. Does the WinSCP patch show as failed in your Deployment Tracker? If so, that's almost certainly what happened.
Let me know if that helps, or if you open a support case for this (I'll make sure I take that case). I'm happy to help however I can. One thing I would definitely recommend on machines like this is to schedule the reboot for a specific time of day - that way, if something like this does happen where one patch delays things unexpectedly, you won't reboot in the middle of the day, but overnight the next night or whatever you configure.