Install CFW on Switch, use a save manager homebrew to export the save from your Switch.
Then, use the save on PKHeX.
you can inject an emulator's save into 3DS/Switch, then send to Pokémon HOME.
Cannot send from emulator straight to HOME. Need to inject the save first.
Already known; certain existing features don't play well with the new upsized sprites.
https://github.com/kwsch/PKHeX/blob/master/PKHeX.WinForms/Resources/text/changelog.txt#L19-L20
https://github.com/kwsch/PKHeX/commit/bf47317dd1616153e7be5bb85ab641f1cb3ede1a