First of all, an upgrade means new versions of almost everything.
If your compiled code (C, C++, Fortran) doesn't run, start by recompiling (including any libraries and object files). It might be that some older code has issues with current compilers. It would normally be best to fix the code, not to downgrade compilers, but if necessary, some older versions of compilers are available through environment modules.
If you have python venvs, conda environments or personal installs of python packages, it may be necessary to reinstall those. The current system has python 3.9 as default version (previously, there was 2.7 and 3.6).
Other versions of python are available through environment modules; conda is present already on the system. Please use the existing conda installation if possible. This version doesn't require any settings in .bashrc or .tcshrc.
On the new system, we have a greater range of available desktop environments to choose from; Gnome and Cinnamon are now there in addition to Xfce and Mate.
There are some known issues with the desktop file managers in Mate (caya) and Cinnamon (nemo).
If you have linked your desktop to cloud storage such as Google drive, Dropbox, Surfdrive or Nextcloud, you will get some timeouts on login since these services are not (yet) working on the vdesk system. After a couple of minutes, desktop icons will appear and everything will work normally (except of course the missing cloud storage). Everything else (menu, applications etc) will work normally, even before these icons appear on screen. There are no known workarounds at this time.
This filemanager will crash on startup (perhaps for the same reason as the nemo issue mentioned above).
There is no complete workaround yet, but luckily, Mate allows the selection of another filemanager. To do this, go to the System menu, choose Preferences, then Preferred applications. The file manager can be selected under the System tab. The easiest chooce is dolphin.
This doesn't help for the missing desktop icons, but everything in the Places menu will now work with the chosen file manager, so you have easy access to all your files again.
Not related to the upgrade, but worth mentioning: many applications have problems running simultaneously on multiple systems, from the same home directory. This doesn't play a role if you log in to vdesk from your laptop or home computer, but if you are connecting from a Sterrewacht desktop, you can expect some weirdness in some desktop applications.
Most webbrowsers will have a locked profile, so either make a new profile in the same browser, or use another one (eg firefox on your strw desktop, and brave browser on vdesk. mail clients thunderbird and evolution have similar issues.