The beams aren't being deleted, they're being moved. You're having issues because your beams are not hosted to work planes.

I can only assume that there used to be a work plane assigned but it has been deleted, now when you try to pin the beams Revit doesn't have all the information it needs to pin them in place so it assumes the values it needs and moves the beams.
Place a reference plane in the plane of the beams. Then cut and paste aligned to selected levels (Level 1) to recreated the beams on the work plane. They can now be pinned.
