Legends Arceus "bans" occurs when multiple save files went online with the same sync id. I'm uncertain of that, but I assume Scarlet/Violet having that check too.
Anyways, this would not impact you if you transfer saves from your emunand to your sysnand, for both Legends Arceus and Scarlet/Violet.
Save file playtime vs Switch playtime has never been an issue.
Do note that Scarlet/Violet has been out since very little time, and we still don't know the checking/measures Nintendo/GF could have implemented. I will not say, "go online it's safe". So far, though, with the past games that would not have resulted in any bans.