Yes, indeed. If you improve a weapon with a Tenebrium bar it becomes a Tenebrium weapons. If you enhance a 2h weapon with Tenebrium your 2h skill becomes completely pointless...
This is also NOWHERE explained in the game. At first sight I thought it was a bug because the bonus from 2h weapon skill wasn't added to my damage until somebody explained the Tenebrium skill to me.
This is imo a real design flaw, especially because it makes no sense at all. If you improve a weapon with Tenebrium the additional Tenebrium damage is rather weak (on par with elemental damage). If you have a traditional weapons skill (like 2h) on level 5 and Tenebrium on level 1 it's actually a no brainer to NOT enhance weapons with Tenebrium or to NOT use Tenebrium weapons at all. I mean, why putting tons of skill points into Tenebrium if it only adds like 20-50 damage to your weapon and you already have a high traditional weapon skill? Makes no sense at all...