I will start with some informations, then i explain what happend before the problem i run into.
(if i speak about 2 Skins i mean the CollectorsEdition PreOrder bonus you get ingame)
I bought the game using the Shop from Egosoft, so not using Steam (if this is relevant in any case....).
I preorderd the CollectorsEdition, so i got 2 additional Skins for the Spaceships (the 2 Skins are the reason for this topic).
The Game has been started the first time on 2018.12.04 at 22:30, dunno which Version it was at this time.
The Game has not been modified.
I checked the Settings and that there is an online function, because of that i logged into my account on egosoft.com and registered the Game using the "Update via Steam" Button.
After that i started the game again and linked it to my account, then i tested the game, and also discoverd that i had 3 Skins for my Spaceship (the default, and the 2 additional ones...).
So it worked.
(by the way, i never played the game a long time, so i never saved my progress...)
After Update 1.30 (3230986) i started the game again to test and discover the game everything was fine (related to the 2 Skins),
then i quit the game and changed it to run as betaversion (1.31 beta 1) everything was fine there too.
I changed the Skin of my Ship to one of the 2 Skins, then the game crashed (i dunno the reason).
After restarting the Game the 2 Skins wasn't available anymore.
I changed the game back from the betaversion to the stable version and relinked (ingame logging out and logging in again) but the 2 Skins are still missing.
The following Topics descibing a similar problem (if not even the same):
Pre-Order Paint Mod
Unable to login Online Feature for X4
Greetings
DMI-1407
PS: Where is the attachment functionality ?

If somebody needs the dmp-reports or informations about my System i can provide dxdiag and msinfo32 them via PM.