I highly suggest you start from a fresh image. That zz-kolibri-upgrade may have installed files that are not meant for the Pi architecture or overwritten some of those fixes that are implemented on the pi.
You can back up data from within a working Kolibri facility by putting in a USB stick and then exporting it. On the new device/Kolibri facility you should then be able to re-import that.
The very large data you have, Wikipedia and Wiktionary, are you restoring these using WinSCP? This shouldn’t take days to install over a local network. It should take about 20-30 minutes depending on the speed of the MicroSD. If you are re-downloading these files, I suggest you back them up to a PC and then use this tutorial as a guide in transferring them back over to a freshly installed RACHEL-Pi on your 256GB card. That tutorial also contains a few tricks to increase the speed of a transfer greatly.
Since you’re so close to deployment, a very important one it sounds like, I really suggest you start with a fresh image, try to export/reimport your Kolibri data/channels, back up your large modules to a PC, and then transfer them over again with WinSCP.
The upgrade process of Kolibri itself is somewhat risky, I always recommend a straight upgrade to a new image for these kinds of things, but there won’t be a new image available for a few weeks. It is well known that if an update isn’t done properly it can cause a database corruption on some devices. What my updated installer would do is remove the existing installation and do a clean install of the latest Kolibri, but it’s still somewhat risky and untested. I don’t suggest doing this yet.
Please let me know if any of this works for you, if you need help with that process, or have any other questions. I’m very happy to hear your pis are working well with the supercaps now and going to such a great deployment. Great work!