There is no reimbursement for FC houses because the house belongs to the FC and not a character.

Before you can initiate a world transfer for a character, you have to turn over leadership of the FC to another character and have your character leave the FC. Or you have to disband it but before you disband a FC you have to relinquish any house it owns.

You're pretty much out of luck here when it comes to getting any gil back for the FC house if you're going to take advantage of the free transfer. If the auto-demo timer was active, you could have locked everyone out of the FC house and chosen not to enter it yourself for 45 days so it would demo. Since it's currently suspended, you can't use that method prior to the free transfer period ending.

Your best bet is to try to find another player who isn't going to transfer and would like to take the FC over. Maybe they'll be willing to give you something as compensation for what you invested in the FC but that would up to them.