kalron: Hey thanks everyone! Honestly in the end I just booted it up to my last save (Which was on my Cruiser at the point of discovering ships missing) to try some of the suggestions left here and the ships were there on my reload!!! Looks like a reload, regardless of the instance, will restore bought\acquired ships. Yay! Problem solved. Here are some images of the ship I was able to restore, I couldn't ask for a better even with a ship mod patch :)
Check out the name on the last pic...I swear I didn't change it, why would I?!?!
Nice ship. Glad you got it sorted out. Just be warned if you do a series of saves/reloads on a planet (if, for example, you're trying to spawn a specific ship as S class at a trading post), your other ships may disappear from your freighter. But warping, calling, or reloading on your freighter will fix it. And whether they're there or not, you can still call them down to the planet surface.