This is the first time it happens to me and I'm really ashamed. Before installing the new version of discovery I played the single player mode thus resulting in one retail freelancer copy and the discovery one. My account manager backed up the data from the retail one making me believe my account was safe. Today I uninstalled the retail version since I no longer needed it and so my account got lost in the void.
The ships were:
Col.Dem - Outcast Gunboat -outcast id in Omicron Alpha
Haris_Pilton - Dagger -lane hacker id in NY
Hinder_Pilton -- cant remember, used it for test restarts
jfkrolling -- same as above
J.K._Crawling - 2k transport with DSE id in Pensylvania
I can recreate the account with the code and signature only if I could get them back. Thank you for reading and sorry for troubling anyone.