I'm getting the same thing on the original save file now.
Think it's because those missing chunks had items contained in chests that MC didn't like, so it's regenerated the chunk.
My best advice at this stage would be to download the schematic files and place them one at a time into a flat creative map for repairs if you're desperate to use them.
I'll get round to repairing them with time and upload a repaired shipyard.
EDIT: K after some testing, this is the current situation:
MC eats ships it doesn't like. =]
The schematics will load "correctly" ONCE into world - the trick at that point is to make repairs in one hit and hope that MC likes what you've done.
If you didn't remove/repair the offending item/block, it will eat the chunk on world save and appear funky on reload.
Will have to work on one ship at a time I guess T_T
The good part is that the individual ship modules seem to pass the chunk test ok - with the exception of modules containing more complex machinery or ore processing.
The farm ship is a bit of a mystery to me though, there's not much on the thing.
I'd start by deleting the personal safes, reckon that's a big part of it.