What version of Jamf Pro were you trying to upgrade to, and were you able to resolve your issue?
There is a known issue with the Windows installers PI-007299 listed in our Jamf Pro Known Issues where the Java option
Djava.endorsed.dirs prevents Tomcat from starting and we will be fixing this in an upcoming release of Jamf Pro.
@ngidzak I'm not sure if you are in a Windows environment so this may be irrelevant. You may check these two things to see if it solves your issue:
Steps 4 and 5 here:
The note under step 2 here: