quick answer:
As you are already tier 69 any other "quest" upgrades you want to do are no problem at all, you are already above that tier, and your ship wont be downgraded.

full explanation:

ok, here's a little bit more indepth explanation of what happens, but before i do this, i need to explain a little bit about how the game works.

Once you start your character, a image is loaded, which contains the buildup of your ship, with one pixel per block. Then another config file tells the game what color should become what block. It tells what background image (the outer hull) is to be used.

The config file ALSO tells the game what block are non-destroyable. Like the shiplocker, the s.a.i.l. teleporter and the captains chair. This is unreversable within the game. Once locked down there is (i have not found) a way to make these deletable again. And herein lies the crux.

B.Y.O.S. upgrades your ship to tier 69, way above the max current tier. It does so using its own block and config files to bypass locking down the items as described above. Tier 1 to 8 are identical to the original vanilla shipfiles, with the exception that the blocks are NOT locked in place. As a side note, because they are not locked, the fall off at the first upgrade. This is the reason the quest gives you a manual set to use.

For easier reference from here on, shipblocks are blocks and items placed by the game, playerblocks are placed by the player.

Now, if you started out your character with B.Y.O.S. installed, there's not issue, as nothing got locked down. The upgrade to tier 69 will replace all the shipblocks, and all the playerblocks stay, provided that they are not attached to shipblocks (a locker on a wall will fall down if the wall disappears, it will be retrievable though).

If you did not have B.Y.O.S. installed when you started your character, the 4 items will already be locked down, nothing in game can fix that as far as i know. The ship will upgrade to BYOS, you can do what you want but the 4 items will have to remain in place.

There is a way out of game to fix this. This will delete everything in the ship though, so make sure you empty it out first. Exit the game, go into your player folder, find the corresponding shipworld file, and rename it (so that you have a backup, if you dont want a backup you can delete it).

Upon starting the game with that character, the game will rebuild the .shipworld file by going through all the tiers again, it will basically be upgrade to tier 1, tier 2, 3, 4, 5, 6, 7, 8 and 69. You now have a clean ship that you can totally remake as you want.

Thats great ! Might want to do a tl;dr at the top tho even if thats great stuff to know. I was asking because of the upgrade quest but also because tenants placed on ships scale based on its tier so i wasent too sure. This should totally get pinned or something

is there a way to revert from tier 69? when i did the quest my ship did not change, and because of parsing issues(powershell hates the "inf" value) i can't recreate a json with tier 8 as the ship