During a certain patch beta, i was abe to use a Craver "Prime" reskin, and when returning to the actual game I was not. Is it possible to get this reskin for the base game somewhere? 

I'm not 100% certain on this but I believe the only way to get the Cravers Prime skin was to buy the Digital Deluxe Edition While the game was in early access,

As it was part of the Founder bonuses in the Digital Deluxe Edition.

So I think that there is no way of obtaining it currently if you do not have it already,

But they may do something with it later on to have it unlock for everybody (maybe on Endless day?)

I would pay pretty good money for it too.

What confuses me is that I have the Digital Deluxe Edition but I no longer have Cravers Prime ships. And yes, I did tick the box in the lobby to enable it.

That's odd, They work for me.

But I'm on the 1.0.49 Preview build,

Try the preview build and see if that fixes it.

If not make a bug report about it.