Managing "configs" is much different, and it should be quite possible to have one config for a mature project and others for more active experimentation. Depending on how long ago you had an error where settings were lost, it's possible that improvements have been made to the way configs have been saved. Also, I know there's new development which will hopefully make balancing multiple configs in a project easier in the future.
But back to keeping the actual PT text static, which seemed to be your main question.
Here is what I would do, as it seems most straightforward (to me).
1) Create another folder for static projects. As an example I'll say it's at c:\temp
2) Copy your XYZ project to the c:\temp folder
3) Run ptxprint from the command line (or create a Windows shortcut), using this command: c:\Program Files\PTXprint\ptxprint.exe -p c:\temp
(note that I don't have it installed on Windows at the moment, so I'm not 100% sure that's the right path). This basically tells PTXprint to open up inside of the c:\temp folder rather than the normal My PT 9 Projects folder.
4) Should you ever need actual text from PT updated in your printing project, you'll need to manually copy the relevant file(s) from c:\My Paratext 9 Projects\XYZ to c:\temp\XYZ
Also keep in mind that your configs aren't being backed up or shared via PT Send/Receive anymore, since they're living inside the detached c:\temp\XYZ folder.
-------------------------------
Step 3) could be replaced by the following, but I suspect that simply copying the entire folder would be easier.
a) create an archive of your project inside of PTXprint
b) Run this once to expand the archive to that temporary directory: c:\Program Files\PTXprint\ptxprint.exe -Z archive.zip -p c:\temp
This will probably result in much less information being copied over, but possibly not enough. I think if you have hard drive space, that simply copying the entire folder would be better.