Well, .DeleteItem was my first thought, but it caused the usual problems like either deleting the script or even kind of freezing the game.
To prevent this I also could set the .DeleteItem command to the end of the whole "combining item function", but that seems not possible for me when my playing character comments the action with Talking -- it would look very strange if the actor said something like "got it!", adds another paragraph of monologuous comment and then the change within the inventory would be seen... that would look awkwardly unnatural...
... so I decided to use the second workaround method with disconnecting the item relation. Primarily this would solve the problem when I use .DropItem, but when I use .DeleteItem the command still freezes the game. :/
Therefore it really seems to me I should achieve to keep the state of the changed scene entities when reentering the scene -- which does not work properly yet.
EDIT: Also I have to delete 2 items in one action -- so putting the .DeleteItem cmmandS at the end would not work, I guess, since the script would stop before the second item would be deleted...