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Naturally, there will need to be some translation of the various things that your character has accumulated over her life, and reputations are the trickiest of these. While your home faction will be switched to the one which correlates to your new race, all other reps of the Alliance or Horde will change according to the following chart:
Darnassus - Undercity
Exodar - Silvermoon City
Gnomeregan Exiles - Thunder Bluff
Ironforge - Darkspear Trolls
Stormwind - Orgrimmar
Your faction-specific achievements will be easier to switch around, although there is one very important caveat here. From Blizzard's FAQ,
"With this, completed quests that are considered faction-specific—or are faction-neutral and part of a quest chain—will be removed from the list of completed quests and no longer count towards any running 'quests completed' totals."
What that means, for completionists and those currently working on a quest-related achievement, is that it's better to wait until you've attained your goal or be ready to start all over again. If your character is 2900/3000 toward reaching "The Seeker," understand that the completed number will drop substantially following the transfer.