My first answer: very carefully.
this isn't the first and won't be the last time you encounter something like this. I just ran into this same problem with two Thomas Gardner families -- one from Salem, the other from Roxbury. 1600s. Their kids were mixed up; they both supposedly died the same day (not) etc etc.
First, read the narrative and the changes tab to see if anyone has been working on the profile recently. Someone (like me) might be working on merging dupe profiles of early New England colonists. Coordinate efforts if someone is working on the profile(s) in question.
Then, find the most recent and thorough research on the line. For colonial New England it's likely to be Robert Charles Anderson's Great Migration series or research done by Jacobus and a few others. NEHGS Register and The American Genealogist are two excellent journals with sound research and published vital records. Be wary of genealogies published in the late 1800s.
Next, I create a Word file in which I compile the correct information for each family.
Using the Word doc as a guide, start teasing apart and putting back together again the families in the correct configuration and right vitals. Merge dupes to the lowest profile #. Ask a supe to lock the results so the completed and accurate profile cannot be merged away.
Be sure to include in the bio section -- right at the top -- an explanation of what happened and what you did. I will often include links to the "counter" profile(s) as a way to acknowledge and clarify the confusion. See http://www.wikitree.com/wiki/Gardner-611
As an example. Contact me if you need help with the early New England folks. I have access to all the resources I mentioned above.