Basics from off the Pokemon website itself, in plain English and short and sweet:
- you cannot erase a game once linked and if you reset the game card after linking it can no longer be used with the account, you will have to sync the new game with a new account.
- you can look up the ID of the synced game in your VS Recorder device. Going into the account online you can match it up to the synced ID.
In sum, it's actually a pain to sync the games... One account, one version of each game, and you can't restart a game, or you lose everything online as well as on card.