OK, with Ship Storage Helper 0.28 and Ship Respray 1.2.1, this is what I get. Please confirm that the same happens to you if you follow these steps:
1. Load a Cobra III savegame with an empty cargo hold. Make sure you have the Large Cargo Bay installed.
2. Go to the F8 screen and buy 35t of whatever.
3. Check that your F5/F5 says Cargo 35 t (35 t).
4. Go to the F3 screen and select Ship Respray.
5. Select Respray Style 2 and buy it.
6. Now, without exiting the game, check your log file. At this point, mine contains this:
14:13:46.680 [Oolite Equipment Control]: The large cargo bay was removed when there wasn't enough spare space to contain it.
This is probably due to an OXP failing to validate cargo bay removal before trying it. The cargo bay has been restored to prevent inconsistencies
7. Save the game to a new file.
8. Check again F5/F5. It should still say Cargo 35 t (35 t).
9. Again without exiting the game, load the savefile you just created.
10. At this point, I find that the F5/F5 screen says Cargo 35 t (50 t). This is obviously incorrect. The equivalent of another cargo bay has been added to the cargo capacity of the ship.
For me, this happens only with Respray Style 2. Respray Styles 1 & 3 are just fine and their savegames load without issues.
I think that what you are experiencing is very much related to the above. The warning quoted earlier comes from the built-in script oolite-equipment-control.js and is there to prevent removal of cargo bays when the ship is full, which is most likely what Respray does when swapping ships.
Edit: Looks like step 2 is optional. The same increase in cargo capacity happens even if you don't buy anything.
Edit2: Seems that the issue is caused by the Respray Ship script awarding a cobra3-alternate ship for respray style 2, which is defined to have a 35t capacity by default (the others have 20t), so when the game reads the savefile and sees a cargo bay, it goes ahead and adds 15 tons to the base 35 ones.