I guess this is related with latest enhancement "Sections: Sort and search parameters of each section of each opened notebook are now remembered".
I think it actually gets saved because I have this in .settings:
viewstate.notebook[2643a8c0-84f3-420b-8f0f-37940d89e402].section.sorting = modified
If I take .exe from CN 2.0.1, sort order saves again, but uses view.sortby setting instead.
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