I already mentioned this in my blogpost about Exchange 2016 CU6 and Exchange 2013 CU17, but when upgrading an existing Exchange 2016 server to Exchange 2016 CU6, the setup application stops after step 5, 6 or 7 (random) with the following error message:

“A reboot is required to complete file operations on ‘E:\exchangeserver.msi’. Reboot the machine, and then run setup again”

After rebooting and restarting the setup application the upgrade finishes successfully.

Rebooting the Exchange 2016 server prior to starting the upgrade process does not prevent this from happening. Also, there’s no difference between Exchange running on Windows 2012 R2 or Windows 2016.

The installation process has been tested by Microsoft and TAP customers, and tests are still conducted. It is somewhat clear what the root cause is for this issue, it is an MSI package that’s causing this issue. Please be aware that the Microsoft setup application executes around 200 MSI packages, and if only one MSI package is having difficulties you can see issues like this. Because of the number of MSI packages it is not possible to check in advance if your server will experience this issue.

At this moment the only solution is to reboot the server when requested and restart the application program.