Merging tree lost ancestors.

ATTENTION curators. Please join discussion if possible. A friend originally created my family tree. She used my Grandparents on my mother's side. I created my own tree and purchased Geni Pro. Geni asked if I wanted to merge my friends tree containing 5,000 ancestors with mine. I clicked yes. All of my Grandmother's family and ancestors migrated to my tree but all of my Grandfather's ancestors disappeared.  Even if I go to the tree my friend created they are all gone. Thousands of them. So much work went into it by my friend it is devastating and so much was lost. HELP!