http://na.finalfantasyxiv.com/lodest...nsfer_service/

This pretty much covers everything it will and won't affect. Pretty much if it's character data and not tied to the world (like an LS/FC/friends list/estate), it will be preserved.

Quote Originally Posted by REPROBEAN_CHILD View Post
Will my story progress, dungeon unlocks, Gold Saucer cards, items, and other things be safe as this happens?
All these things listed will be safe, unless by 'card' you mean 'tickets'.

The following will not be transferred along with your character:
Friend lists
Blacklists
Linkshells
* Transferred characters will be removed from linkshells automatically.
Free Companies
* The World Transfer Service cannot be used for characters enlisted in a free company. Please make sure your character is not a member of a free company before using this service.
Housing
* Ownership must be relinquished before World transfer is made possible.
Scores from currently entered Triple Triad tournaments
Scores from Lord of Verminion tournaments
Jumbo Cactpot tickets purchased prior to World transfer
* Any tickets purchased will be lost upon transferring.
Season Rankings from the Feast
Ranked solo matches
Matches
Victories
PvP rating
Tier
Progress during promotion qualifiers
Ranked party matches
Matches
Victories
PvP rating
Tier
Progress during promotion qualifiers
Deep Dungeon Scores
Personal High Scores (All Classes/Jobs)
Party High Scores