Zuzu worked with the merge tool a lot and gave me some pointers. She said "the merge tool only moves photos and comments and will only move them to the entry with the lowest ID number. If the one with a higher ID number has plant growing data, you have to add it to the other entry before the merge. You also have to correct the names on the entry with the lowest ID number before the merge because the merge tool won't combine names either."
So often it's easier for admin to manually take care of any photos, details and add to synonym names before deleting that entry. When you find these, it's best to start a thread here in the Plant Database forum and then any admin can take care of it.