The Higgins=Robin Masters plot thread was clearly an invention for the final season, but that doesn’t completely invalidate it.
The early episodes can be reconciled with the final season if you look at it as a Remington Steele type situation. In that show, Steele was an invention used by a highly competent but not well regarded private detective Laura Holt, who needed a flashy front man to get attention while she worked behind the scenes. A con man (whose name we never learn) latched onto the fictional identity as a meal ticket, and came to like it enough to stick with it.
In the case of Higgins=Robin Masters, Robin Masters is the flashy front man used by Higgins originally to draw attention while Higgins did the real spy work. When Higgins retired from the spy biz, he continued to use Masters as a front man for his ghostwriting, so that Higgins could lead a normal life.
In this scenario, Masters is a real person who serves as a front for the real commando/spy/writer Higgins.
Or you can just pretend that that final season didn’t exist. I like this option, if only because the final episode of that penultimate season was so much better than the finale we finally got. When it was filmed, Magnum had been canceled, and the episode was intended to be the series finale. CBS renewed Magnum for one more season at the last minute, and a brief intro to the episode was added, explaining this.
What I liked most about this was a subtle (for a tv private dick show) effect that was used at the beginning. Every episode of Magnum has a voiceover by Magnum, in character, in past tense, in the first scene in which Magnum appears. This is the film equivilent of the first person narrative of most detective fiction. First person narrative carries with it the implication that the person telling the story survived to tell it (notable examples such as Sunset Boulevard and American Beauty notwithstanding–in both cases the narrators tell you they’re already dead at the very beginning). By removing the introductory voiceover (it was instead replaced by an amplified heartbeat as an outgunned, nearly out of ammo, Magnum is trapped in a warehouse by armed thugs), this subconscious reassurance was removed, but it wasn’t until after Magnum’s attempted escape from the warehouse that we realize what it was that was missing that made the scene more tense than usual. That and the knowledge that the rules go out the window in series finales–title characters can be killed (on Buffy, this is true of every season finale).
And the final scene was a perfect end (for Magnum). As trauma surgeons try to revive Magnum, he walks off into the clouds. Higgins orders him to come back, and Magnum looks back over his shoulder, then walks away into the mist. It fit so well as a final commentary on Magnum’s character and his relationship with Higgins.
The final scene we got instead (Magnum walking on the beach holding hands with his daughter), though pleasant, didn’t fit the character as well.