So I did recreate the ship. It does correctly adjust BP now if I create or delete an item, the issue with the added or upgraded weapon mounts persists but I guess I can work around it by adding these items manually. Although now I found a different issue; when calculating PCU consumtion it factors in the Drift Engine
Attachment 40282, although a drift enginge just has a minimum PCU the ship needs to provide in total and no consumption (at least thats how I always understood it, correct me if I'm wrong). CRB.298 for reference here.