So, I transferred my main over to see what effect it would have on the character. Here's what I noticed happened:
First the money part. As far as I can tell, EC and GPL were unaffected by the transfer (no shock there).
Pre-transfer I had the following:
Marks - Exploration 17, Valor, 2, Excellence 94, Distinction 25, Bravery 36
Badges - Fifth order 150, Third 32, Second 75, and First 35
Post transfer: 97,262 refined dilithium (that's REFINED)
Now in the C-Store it gets a little weird. I had already bought Excelsior and Nebula pre-transfer. My nebula that I fly was converted to the new +1 version (sweet, I can swap out the Tachyon Grid!). I also had "purchased" the Intrepid Retrofit with my VA token. All three ships were available to me without any problems (though I had previously claimed all three with this character).
Problem 1: I no longer have access to the T3 versions of the (C-Store) ships. Since seperating them, apparently I'm not cool enough to have both (even though that is what I purchased)
Problem 2: All my bridge packs have disappeared. The C-store (and ship editor) makes it appear that I have to rebuy all of them. Funny quirk, if I beam to my bridge, it's still my purchased one.
Problem 3: My purchased clothing items are gone as well. The one I know for sure is the open jackets, which is no longer an option. Again, my BOff who is currently wearing it still it, but if I try to select it on any new ones, it asks for money.
Problem 4: Ship costumes are missing. Apparently it's all the vanity items that are gone.
That's all I've noticed so far. Feel free to post any other things you've noticed in conversion or if your items are missing as well.