While you probably will never be put in this position, sometimes for tournaments trainers need to submit an amiibo that doesn’t fit a ruleset. To compensate for this, they’ll scan their amiibo into an editor, add or remove the stats and moveset, and then send the .bin file to the tournament.
Changing an amiibo from vanilla to customs by adding custom moves, stats or bonus effects without training them for a few matches before submitting them is very damaging to how they play, and they most likely won’t perform very well. The reason for this is pretty self-explanatory. If you woke up one morning and you were suddenly two feet shorter and spoke a different language, and you had, say, a piano recital, you’d be pretty darn confused too. Amiibo are the same way. They’ve had no time to get used to these new moves and stat changes, and now they have to use them against an opponent that is very comfortable in their own skin.
Going from customs to vanilla is generally less difficult, but it depends on a variable or two. As a rule of thumb, the more non-vanilla moves and stats the amiibo had before, the more difficult it will be for them to transition to vanilla. It’s almost kind of funny watching an amiibo that previously had three or four custom moves. They struggle and struggle, because now they have different moves, and on top of that their stats aren’t in effect anymore.
Bottom line, don’t transition an amiibo and send them straight into battle without giving them a few matches to get used to it first.