I came here expecting it was the EnderStorage in the ship that got corrupted. It was indeed the EnderStorage that got corrupted. Called it.
Open the blightfall folder > saves > worldname > Delete the EnderStorage folder. I hope you weren't using the EnderStorage for anything, cause that's gone now. Also, no more items flowing through a pipe in the starter ship.
Also, please pastebin that log. Its way too long.