Finally fixed the issue about the fuel hatch. The broken fuel hatch will be replaced funtional one once you finish the crystal quest.

It had some error on ship map file. I discovered while playthrough. I fixed it.

1. Captain Chair Will Never Disappear Automatically
You don't have to relocate it. Captain Chair is still able to relocate. And if you relocate it, it will spawn again. Both will functional.

2. The Broken Fuel Hatch Can Not Be Possibly Got Upgraded.
I am not 100% sure about it. But it has the bug that after you upgrade your ship to tier 3(Fixed FTL Drive) the fuel hatch still remains in the broken state. I fixed the map file so I think it would not happen. If it happens please use the console command :

/admin
/spawnitem humanfuelhatch