Losing abilities... sounds very much like the double click bug, which they are working on. It's unclear at this point whether a fix will be retroactive though.
I'm not sure if re-adding them via console would be 100% safe with a patch so probably best to wait and see when they release the patch.
So what should i do ?
Wait for the patch. Add manualy the abilities ( but which one) ? Or begin a new game, i already played 21h on this game.