Docker Qube

I have created a docker cube to run a node for Presearch. I have been running one for 3 years but when updating to the 4.1.2 version was I having problems.
I could install Docker and get it working in a Fedora qube, it worked fine until I reboot the computer and then I could not restart the docker some files that I know I installed were not there?
To solve the problem I had to install a qube type TempletVM (templet home, persistant root), when I did that I got a pop up telling me that was a very bad thing to do. I don’t do anything in that qube but run docker. Am I compromising my system?
I can live with a compromised qube but I do not want to compromise dom0.
When creating a new qube with volatile root what exactly does that mean?

This is not very useful. The exact wording of the error would help us to help you.

Open the Settings of this qube, tab Advanced and look what is chosen as Virtualization mode. If this is PVH then you are probably safe, since this kind of virtualization is very strong. You should use HVM if you attach any devices to this qube. PV is not recommended and less secure. More details: Standalones and HVMs | Qubes OS.

This looks like those file are not persistent: Templates | Qubes OS. This should help: How to make any file persistent (bind-dirs) | Qubes OS.

Use a TemplateVM to install Docker and all the necessary programs you need, then create a new AppVM based on that template. As for the missing files, my guess is that you’re using classic volumes that are located in /var/lib/docker that are not persistent. Have a look at docker bind mounts and mount them somewhere in /home/user/ so they are available or use bind-dirs as @fsflover said. Also, note that docker isn’t started/enabled by default on Fedora, run this command in the template to make sure it starts when the AppVM boots:

sudo systemctl enable docker