That generally sorted out those sorts of problems before. Digging into the forum will show a fair bit of discussion on this issue.
Have you looked outside the zynthian community for settings ? It can get a bit, as you describe it, magical but that might flush something out…
All I can contribute is it used to be a right pain and if you did get it right it would reset when you powered off, but this is the first mention of it that wasn’t addressed by the tool.
In my reTerminal, I had the same problem. I fixed it editing the file /usr/share/X11/xorg.conf.d/40-libinput.conf. There, look for the section InputClass with the Identifier libinput touchscreen catchall, and in that section, add the following option: Option "InvertX" "1". The whole section would be as follows:
step 1 - get yourself to a Command Line on Zynthian - either “ssh” to Z or access terminal in webconf. If you don’t know how research or come back and ask.
step 2 - get into an editor on the file. vi is available along with many others. If you don’t know how you can find a VI tutorial on the web or in a book. Or ask if you get stuck here.
step 3 - add the section indicated by @oscaracena above.