Home assistant OVA on QNAP

My current HA is running on Lubuntu 19.04, and has been for some time, but recently, I was unable to update it:

You are running an unsupported installation. Learn more

Your installtion is running in an unhealthy state. Learn more

So, I installed HA using the OVA, it worked fine, until it came to update it. The HA updated, but then it asked for the OS to update - I did this, and it then failed to restart. I forget what was on screen, but it didn’t suggest any problem, just terminated in a yellow prompt. and a message about startup.nsh I think.

Still HA wasn’t properly set up(I’m still using the old version on Lubuntu), so I downloaded the latest OVA and set it up.

Before going to the extent of recreating my setup, I want to start over (My HA has been running in one way or another for 3 years or more) I need to understand if it is possible to be able to save my config and reapply it if I have to update the OVA in future. Did I make a mistake by updating the OS when prompted - should I have ignored the request or done something different?

I have Samba installed and enabled - is it just a simple as restoring the files and restarting HA? or would it be better to use snapshots - can I restore a snapshot to an “updated” version of the OVA?