when you select "upgrade" all the old parts will disapear automaticly (makes sense i guess since youre going to upgrade), at least for me, so it's not a problem and i dont have any old parts left at all. It's easy to see too, i check the list above the ship where you can see what parts are there.
I guess it must be some bug

i did install that hi-res texture pack, perhaps it messed with some settings?
Example:
Core collony ship:
3x basic support
2x colony module
1x hyperdrive (size 21)
Ship-i-want-to-build-but-cant: (same hull since i just use "upgrade", all parts are 100% cleared.)
3x basic support
2x colony module
1x hyperdrive plus (size 18)
Ship-i-can-build-without-it-complaining:
2x colony module
1x hypderdrive plus
if i try to put just 1 basic support (compared to the 3 the original has) it'll just tell me its too large!