Well, took me a bit too long, I can answer my own question now. Leaving it up for anyone returning who may run into the same issue. Change a clan hall to the spawn location at the room terminal and then you can destroy any other room all the way up to the new spawn room. Start from scratch again but definitely use a dojo planner so you can take into account the different levels that may be needed for larger rooms like Drydock.
For completion's sake, all the materials (including platinum you may have used to rush) will be returned to the vault. No, you cannot take materials out of the vault but you can use them to rebuild rooms, decorations and rush a room/connector/hall.
Lostara's post in Yet another dojo question >.< was marked as the answer