For what it is worth, I was trying to go from 5.3 client to 9.11r4 client. I have been having quite a few issues with this. I spoke with support who gave me instructions to perform a deep clean. Needless to say, the process required some manual steps or at least I could not fully automate the process.
I decided to just start uninstalling one of the Pulse applications at a time to see if I could perform the upgrade in place as we have done in the past.
What I found was that the Pulse Setup Client application was the issue.
Using my RMM tool, I created a script
taskkill /IM Pulse* /f <-this needs to be run under admin rights. I have this run under one part of the script
rmdir /s /q "%appdata%\Pulse Secure\Setup Client" <- this needs to be run under the user context.
The script is not perfect by any means as it does require a user to be logged into their machine however for the majority of my users, they do not log out of their machine when they are done for the day.
Once the script is run, the user will launch/connect to Pulse again and the upgrade moves forward properly.
Hope this helps your situation.