Try to simply proceed:
This mechanism was introduced by Jolla in SFOS 3.4.0, and when upgrading to v4.0.1 it uninstalled those packages and disabled their repositories automatically.
The changelog for v4.0.1 does not state that this mechanism was changed (which is what you used when starting the upgrade).
For v4.1.0 also no change is denoted, except for the displayed messages.
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