In my work-in-progress, Empress & Soldier, the last third of its story overlaps with about a quarter of my third book, Empire’s Exile. In Exile, we see this section through the eyes of the narrator, Lena, and the characters of the soldier Druisius and the Empress Eudekia are peripheral (although very important) to the story.
But Empress & Soldier is told through the alternating viewpoints of Eudekia and Druisius, and so we are seeing the same events through different eyes – and discovering some those events can have very different motivations and interpretations. That’s not the problem: I enjoy exploring the ‘what ifs’ of different perspectives. But everything that happens in this section of Empress & Soldier must fit the chronology of events in Exile. Actions must occur within a framework that is set. Just like a real historical novelist, I can’t change what has already happened.
For me, working within this constraint is a huge challenge. It’s not how my brain works. I’m used to saying ‘oh, look, I really like how The Battle of Maldon is described, so I’ll borrow that but change its outcome.’ Now I can’t even change a conversation, a dinner served, a walk through the city. At the same time, these things are now background events, most happening off-page. My focus is on what Druisius and Eudekia are thinking, doing, feeling, learning—from and alongside the actions and events that already exist.
Which is, of course, what writers of real historical fiction deal with, in every story—and the more recent the history, the more records of events, the more constraints there are. I am not sure I could do this for an entire book, let alone more than one!
This is how I’m handling it: by a detailed analysis of each chapter (and each scene) in Exile that is reflected in Empress & Soldier. This is an exacting and layered process that is very different from the creativity of writing, and is remarkably tiring. But it must be done, and once it is, my mind will switch back to writing mode—and another challenge: how much of Lena’s story do I retell? (Enough for a new reader to understand what’s going on. Not too much, or I risk boring a returning reader. A fine balance.)
I occasionally consider writing a novel based firmly in historical fact. To save my temper, my hair, my liver—and perhaps my marriage— I don’t think I will.
marianlthorpe.com 
That is definitely one reason I will never write historical fiction that’s longer than a couple pages!
I’ve run into a little of this issue in some of my novels where I’ve had overlap, but for me, I’ve always had a lot less overlap. Though, in one case, I knew I was going to write the other novel when I got to the places that had overlap in the first one, so I was able to write the first one with the overlapping novel very much in mind. Though it might have worked anyways. In another case, I’m writing two such novels concurrently, so I’m going to try to have some of my beta readers read one first, other beta readers read the other first, so I get a better idea if they can be read in any order, which is a must.
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