I created a mess with a merge

I have been working on a line of family with the surname Scott, and at one point there were 2 family groups mixed up because the fathers were both John Scott. There were 2 wives married to him at the same time, different children and 2 sets of parents. I was able to recognize most people who were not part of "my" family group and disconnected them. The only problem remaining was 2 men named John Scott, one with no middle name and one with a middle name. I thought merging them would be the final piece to the puzzle, but when I did that many of the other family members came back, children and the other wife are back as if they were second wife and second set of children. I'm horrified. I'm not sure how to fix this. I've looked at the analysis, and cannot see how to pick them back apart.
Here are the 2 John Scotts: John Scott (K86D-KM3) and John McComb Scott (GZF8-BG9). Their birth years of 1792 vs 1794 are too close to be significant. The child of John Scott who is my ancestor is daughter Nancy C Scott (LCPF-4NY) previously associated with John Scott (K86D-KM3). There is one record with her and her father together, and in it, his name is John Scott with no middle name. Whether the 2 John Scotts had the correct other children linked prior to the merge is unknown to me at this time; I plan to dive into that later. The John Scott who is my ancestor was married to Ann McCampbell (K8QB-85F) and his parents were Andrew Scott (KZQ6-FHY) and Nancy / Agnes Leech (MQL4-ZZ3). There is no Phoebe in my line.
How can I pull these two John Scotts back apart? Thank you in advance. I will probably never merge again.
Answers
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please see private message. Look for the red dot at the upper right by the envelop
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