First, make certain they are the same families and not just families with common names. Beloved grandpa's name can end up on several decendant men with near birthdates.
Provide sources for all of your changes.
If the profiles are open, go ahead and make the corrections. Put a note in the Biography section explaning your source and why you are disconnecting A and attaching B.
If the profiles are public or private and you can't make the edits yourself, put the information with your sources in a public bulletin board message on the profile for each person. Something like, "Please disconnect father Smith-12345 and replace with father Smith-6789 per this source: . . . ". Provide the exact WikiTree ID so that it is easier to complete the changes.