Correct method of migrating database .jar to .msi?

I have been running YouTrack standalone on a windows box for a couple of years using the .jar option. After upgrades the system has always just carried on working but I now need to move the install to a different server.  The preference would be to use the .msi option instead of .jar in the new install but having attempted to migrate everything I keep hitting the same problem.

I backup the existing system, restore on to the new server, and set the permissions.

I then install YouTrack using the clean install option from the .msi and once running use the upgrade option from the bundle/starting path that loads by default after the install completes.

The path to the log and teamsysdata folders is set and the setup process starts. The resulting page simply reports that I should be patient while the system works.

So far so good but the process never completes.  The backup is just 16MB so not a substantial quantity of data but the upgrade process was set running yesterday at 3pm and was still in the same state this morning at 8am.  I've since killed the process, uninstalled and tried again and found that the YouTrack service is stopping almost immediately after the upgrade starts.  If I choose to start a clean install the service continues to run and I can operate as normal (without any data).

Interrogating the event log I can see that the YT service has stopped unexpectedly but does not provide much information.  The event Id is 404, task category (4).

The event itself simply states that "youtrack JetBrains JetService v1.1.730.777 c:\YouTrack\launcher\bin\JetService.exe Service process exited without service stop request"

The current system is running 6.5.17015.jar, the new install is 6.5.17031.msi

Are there any steps I am missing? The issue is certainly related to migrating the existing data but I can't see any specific problem beyond the service halting.

I appreciate I am doing three things at once and will be trying to break the process down as best I can without disrupting the existing system