If you park it at the entrance near the Kaipo desert, then make your way all the way to Damcyan, have you basically screwed yourself over from getting any farther in the game (and making it necessary to start a new game)?
I haven't done this myself, but am at the part in the game now where you get the Hovercraft and that question popped into my mind.
"Looks like taxes are going to go up. Guess I'll have to buy more cheapo ramen". *Random guy in Tales of Destiny*