I'm having some major issues with this bundle! I discarded the Type 10 shuttle to make room for the Yellowstone. Got that, took the engine off of it, discharged it, and tried to claim the Type 10 again. However, it keeps telling me it is still in my inventory. It's not in my ship list, it isn't in my inventory, not in my bank or fleet bank, and I even discarded the pet and Bajoran weapons to see if that would allow me to reclaim things. Nope! This is really infuriating!
Something worked for me that was a bit... odd. Do you have the Tetryon-Impulse shuttle drive in your inventory? If so, put that on a shuttle, then try again. For some reason, doing this allowed me to claim the bundle again. I haven't experimented on other toons in case I was just fluke lucky.
There is a trick to reclaiming the shuttle from this bundle. Here's what you do:
1. Discard the Bajoran weapons.
2. Dismiss the duty officers that came with the bundle.
3. Go to a different map to empty your recycle bin
4. Open the C-Store and reclaim the bundle. Make sure you have an open ship slot.
This should give you everything you discarded back, plus the shuttle. Hope this helps.