Puuhhh, it seems to work again..., but only after a few tries (edit: no it doesn´t > see update).
I formatted the mentioned card with "fat" and put all the samples on it again, but the OT said "ATA FAIL" > OH NO!!!
I stlll have a sandisk Ultra II 15 mb´s for my V-SYNTH XT, so I tried it (just put it in the slot and checked via "TEST MODE" and yeah > "ATA OK".
So I put the original one in there again, which didn´t work and the OT said "ATA OK".
So there seems to be some issues with the CF drive and just in case this happens to anyone, always have a second CF card available to get this bug solved for now.
Update: Despite the fact that it says "ATA OK" for the original CF card that didn´t work I am not able to operate with the card (set restore point/change project/save new project/etc.) again and the OT freezes after that. So I guess I have to wait for my new CF card and see if it solves the problem, because the Ultra II 15 mb´s from my V-SYNTH XT doesn´t work as it is not fast enough.
Thanks for the help and advice anyway!