Yay! 
Our Global Business Team did figure out how to fix this issue (thank you Julia Fox):
1.) We used CS02 to go into the BOM we wanted to delete and extend with the others.
We found the date it was first created and entered that date in "Valid From" field.
We left the Change Number blank.
2.) In CS02, we hit the green check icon, selected "Material BOM" and then "Delete".
This cleared out the change history that we did not clear out before when we used a change number to delete this BOM previously. That change history was what was preventing the extension of the plant's BOM from another after we deleted it with a change number.
3.) Then we were able to go into CS07 and extend the BOM to match the other BOMs, since the change history was deleted.
Thank you again Mariano for your help! We couldn't use Support Note #19006 you found because the BOM could still be displayed (because we deleted it with a change number).