Troubleshooting

start the game, play your bugged character, and close the game
go to starbound\storage\player
sort by date, and rename the latest .shipworld file to .old
then start the game and start your character

If there are still problems, let me know the following in your post:
* What version are you running: see in start screen, click the gear bottom left, and look for the version number*
* What race you play, and if not vanilla if you have the appropriate addon.
* What other mods are running besides BYOS
* If the update does not work, make a copy of your starbound.log file so it remains intact before restarting the game, put it on pastebin and include the link.
Please describe if you did anything else to your ship/mods/game that you think might be of interest.

running frackin universe, did it with that mod before the starting ship turned into that tiny bland ship thing (which is honestly a better more fitting start for a custom ship than that huge wooden platform) and had no issues, the other mods i use should have no compatibility issues. race is hylotl (because ayyy ima weeb and it fits my weeb needs), no other things worth noting.