As you said the elements are no longer in the hierarchy or invisible after reconfig.
Try to navigate on the element PLOOP 1 of PANEL 1 of FRMWORK /PIT-GRATING
There is a chance you may not see this element in the explorer, but you can see this in the old member list form.
If you don't get any error then type q sequence in command line. if the sequence is zero, then patch the database after. This will bring all your elements in hierarchy.