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SBS 2011 Exchange Update to SP3 prior to Exchange 2016 Migration

Hi Team!  We're mid migration between SBS 2011 and SErver 2016. Issue is Exchange specifically.  Following the install path outlined everywhere, Exchange 2010 needed to be SP3, RU 11.  I'll save granular details, but short answer is that took, but the EMC and Shell failed to come up.  I'm seeing lots of EID 2280's and 5139's.  Have done the re-register of exppw.dll, I've reinstalled and moved up to CU 29.  The error's when you open the EMC suggest easy paths to fix. Nothing's working.

Now, the detail that's eating at me..  the error on the 2016 install side that stopped the process was a complaint about exchange 2003 in the environment.  The SBS2011 server started way back as a seperate sbs2003 server and thus old exchange 2003.  It was migrated to SBS 2011 / exchange 2010.   Obviously something hanging out in there.  But on paper shouldn't be the cause of the exchange failure behavior across the network (users can't open outlook with out prompt, owa is sketchy as I'm trying to fix, phones won't connect, emc won't open...)

So, all this said, the bottom line is I've run Exchange SP3 to RU 29 and it's pretty unhappy.  Any guidance is appreciated.
JP
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Saif Shaikh
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What I think here is the upgrade has failed and not all exchange components have been updated.

You can open up a live session with exchange experts so that a tech can review your sbs exchange environment just to make sure exchange functionality like owa, active sync add outlook are working.
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jpbowdoin

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Saif, to address your first comment on removing exchange 2003. The issue there is that the sbs 2011 never had E2k3 on it in the first place.  It was a physical to physical exchange migration (e2k3 to E2k10).  I'm assuming then that the 'leftovers' were part of the migration between the two SBS servers (2k3 to 2k11).
Slight change in behavior. I found this which helped get me past the EMS and EMCPS errors:  https://support.microsoft.com/en-us/help/2028305/error-message-when-you-try-to-start-exchange-management-shell-ems-or-e

Now my issue has changed slightly.  Outlook works again at the desktop. Some, SOME, users are unable to get into OWA.  Credentials are fine, I'm able to login to a dummy machine, setup Outlook ok.  But they can not access owa (and yes, Exchange object is still set with OWA enabled; no change to the user side environment).
Not seeing EID's, thoughts?
What is the error in OWA the users are getting?
Here's where I wound up:

Chasing down EID's 2280 and 5139 found a lead in the XML data.
https://social.technet.microsoft.com/Forums/windows/en-US/89e41ca7-9095-448c-a72d-0d07e6c66207/exchange-2010-iis-not-working-event-id-5139?forum=exchangesvrsecuremessaginglegacy

Manually changing the permissions on the files in the C:\Program Files\Microsoft\Exchange Server\V14\ClientAccess\Owa\auth folder to add the traverse permission fixed the issue.

Saif, thank you for you help Sir!
Welcome Sir.