Matrix (LE10) uses python2, while Nexus (LE11), Omega (LE12), and Piers (LE13) use python3. Our distro packaging ensures the OS update is trivial, but the python change typically causes add-on crashes, so our official advice is to not do any kind of in-situ upgrade from a python2 version to python3 version.
In practice, and if you know your way around the LE and Kodi filesystem, you can drop an LE12 update file in /storage/.update, then stop Kodi, rename /storage/.kodi to /storage/.kodi-old, and reboot to update. This results in a clean LE12 environment, and it's then simple to stop Kodi, copy back essential bits from /storage/.kodi-old/userdata to /storage/.kodi/userdata, and restart Kodi. You can copy addon settings from the previous install, but you need to reinstall all add-ons from repos to get python3 compatible versions.