@rtr2001, thank you very much for confirming this issue on an Xperia 10 III (until now we “only” had Jolla1, Jolla Tablet, Jolla C, Xperia X, XA2 and 10) and when upgrading from SailfishOS 4.5.0 to 4.6.0 (which Nephros already did on his Jolla Tablet): Maybe it is helpful for people with access to Jolla’s internal bug database (e.g. @pvuorela or @flypig) to denote there that this issue did not “magically go away” (why should it, as nothing was altered to address this) and is still wrecking SailfishOS installations.
As @wetab73 already documented very well, the issue with the enormously problematic message which advises users to uninstall packages when using Jolla’s GUI updater is exacerbated by this issue, because exactly that seems to let the problematic message advise users to remove many core system packages of SailfishOS.
As @wetab73 also already mentioned, it is hard to understand, why Jolla has not actively tried to research and address this issue, which seems to exist since the inception of SailfishOS (11 years ago) and is clearly documented and “tracked by Jolla” for more than 5 years.
P.S.: @rtr2001
displayed warning about mapnik having to be removed => went to chum and removed it
Usually this is not necessary, but nobody outside of Jolla knows for sure, because the algorithm to detect these packages does not seem to be documented (at least by source code, preferably by some write-up), or nobody has found that yet.
P.P.S.: @rtr2001
I […] reset the version with ssu (in my case,
ssu re 4.5.0.25). Then rebooted the phone, just in case [, and] started over with “download update”, then “apply update”
IMO this is the best way to move forward, if one knows for sure, that no packages were installed or updated (including the ones which comprise the SailfishOS upgrade) during the period of time in which ssu re differed from version, because installing or updating packages during that time may result in a not working (e.g. not booting) Sailfish OS installation. If that happened, one has to identify the packages installed in or updated to a wrong version and downgrade them to the correct version before proceeding with the GUI updater. sfos-upgrade may work better in some of these situations (but sure not all, e.g. if SSU has become installed in an incorrect version), because it depends on far less other software components to work properly than Jolla’s GUI updater.