The problem I was having is that After applying CU2 it would not update R services and polybase, both services would then shut down due to being at a different patch levels. After digging into the Polybase logs about failure to download various versions of SRO. This is due to my servers being cut from the internet. See below for answer. Exact error message you get will be included once I can reproduce the erorr...might take little.
Reproduced errors using SP1 patch CU2 patch error will look the same with a slightly different download link:
2016-11-23T17:33:38INFOCommand invoked: c:\e140182ad80ef815caf5\x64\RSetup.exe /checkurl /component SRO /version 3.2.2.15000 /language 1033 /logfile C:\Program Files\Microsoft SQL Server\130\Setup Bootstrap\Log\20161123_123235\RSetup.log
2016-11-23T17:33:38INFOValidating URL: https://go.microsoft.com/fwlink/?LinkId=824879&clcid=1033
2016-11-23T17:33:59WARNError validating download: Unable to connect to the remote server
2016-11-23T17:33:59INFOExiting with code 824879
2016-11-23T17:34:00INFOCommand invoked: c:\e140182ad80ef815caf5\x64\RSetup.exe /checkcache /component SRO /version 3.2.2.15000 /language 1033 /logfile C:\Program Files\Microsoft SQL Server\130\Setup Bootstrap\Log\20161123_123235\RSetup.log
2016-11-23T17:34:00INFOSearching for cache dir: C:\Program Files\Microsoft SQL Server\130\Setup Bootstrap\\R_SERV_CACHE
2016-11-23T17:34:00INFOUsing default cache dir: C:\Users\Random\AppData\Local\Temp\2\
2016-11-23T17:34:00WARNC:\Users\random\AppData\Local\Temp\2\SRO_3.2.2.15000_1033.cab: cache file not found
2016-11-23T17:34:00INFOExiting with code 3
2016-11-23T17:34:00INFOCommand invoked: c:\e140182ad80ef815caf5\x64\RSetup.exe /checkurl /component SRS /version 8.0.3.15000 /language 1033 /logfile C:\Program Files\Microsoft SQL Server\130\Setup Bootstrap\Log\20161123_123235\RSetup.log
2016-11-23T17:34:00INFOValidating URL: https://go.microsoft.com/fwlink/?LinkId=824881&clcid=1033
2016-11-23T17:34:21WARNError validating download: Unable to connect to the remote server
2016-11-23T17:34:21INFOExiting with code 824881
Thanks for the hand Shashank