I think I may have said this before in this topic (because I think you've talked about this before), but you'd probably be better off shifting main characters, because then you can basically start the next story with a mostly clean slate, carrying over a few event flags that can be referenced (who's dead/alive, who's dating who, etc).
Continuing the story with the same main character can be fun (and potentially more satisfying for the player), but it can result in you having to juggle all the multiple variables, to the point where branching narrative becomes too hard to deal with, and it starts interfering in whatever story you're trying to tell. If nothing else, it would likely dramatically increase the dev time on the next game.
Weeeeelllll...
The biggest problem with the NTR discussion (especially on this site) is that different people mean different things when they use the word.
I think, when a lot players (if not most) say they dislike NTR, what they really mean is they feel like the player should be allowed to control who characters hook up with and who they don't. When a dev says "It's not NTR because the main character is totally okay with the idea of open relationships and/or a polyamorous orgy", the player is effectively saying it IS NTR because -I- didn't make that decision. -I'M- not okay with the idea of my love interest being with other people, therefore THE CHARACTER I'M PLAYING AS shouldn't be, either.
This only becomes more of an issue when the main character of a game/story is being presented as an avatar of the player/reader. If the main character is YOU in some way, you expect/require the choices that character makes to be more in-line with how you personally see the world. If the main character automatically makes major decisions you radically object to, you're going to feel disconnected from the character, the story, and the world.
In some ways, it's an extension of sexual preference in general. If I'm a straight man interested in playing as a straight male character, I'm probably going to be annoyed/upset if the character I'm playing as decides to start up a gay relationship without being given a choice to nix it (and conversely, when I play games as a female protag, with the intention of playing through as a lesbian, I'm going to be annoyed/put off if she just starts having sex with dudes). You'll see people complain about this in game discussions of games with female protagonists - one of the first questions a lot of people will ask is "Can I play this as a lesbian, or are scenes with guys unavoidable?" What those people are actually asking is "Will I be able to fully control who my character does and doesn't date?"
Sharing or NTR is generally okay if the player is given an option in-game to object/stop it from happening. In those cases, the player may enjoy the scenes even if the character is upset (if anything, that's the whole appeal of NTR for a lot of people). This is where those "Is NTR avoidable?" or "If we turn off NTR does it still happen, or do we just not see it?" questions stem from. Those are players who want control over their character and the world. They want to know that, if they are pursuing their precious waifu, she'll be loyal to them, and won't start chasing after other people. It's also why some people are bothered in harem games where your harem members do things without you (or without your express permission). It's a loss of control as as player.
(And even in real life, two partners being open to polyamory/sharing/open relationships doesn't mean they'd be open to literally anyone their partner might want to date. There would almost certainly be cases where your partner chooses to be with someone you dislike so strongly it leads to arguments, or outright ends your relationship over it. Generally speaking, there ARE going to be conversations along the lines of "Yeah, I'm cool with you dating so-and-so" or "No, I'm not really comfortable with you dating so-and-so" - and those are the conversations the player feels like they're not being allowed to have if the game/dev just says "No, the main character is totally into hiding in the closet watching while their love interest gets boned by three other guys.")
Ultimately, it's up to a dev what they want to do with their own story/characters/relationships/etc, but players WILL complain if they feel like you're taking power away from them (which is the main difference between presenting a story as a story, versus making it into a game with player narrative choice).
Personally, I'd tend to avoid ever making love interests from one game love interests in another game, to the point where a player can potentially wind up feeling like they're cucking themselves. Let's be honest, some people were annoyed when the Mass Effect and Dragon Age games implied love interests didn't stay together after their initial romance ("What do you mean Leliana is off helping the Inquisition and the Warden is somewhere else? What do you mean Isabella is off being a pirate and Hawke isn't with her? WHY AREN'T THEY TOGETHER?!" "Why is Kaiden/Ashley being such a jerk to me in DA2? Well, screw you, I'mma go cheat on you with Tali/Garrus/etc now!"), and even more annoyed when it seemed like a love interest might cheat (people were pissed when Zevran, a notorious sex maniac, could potentially be unfaithful to the Warden with Isabella and Hawke in DA2, to the point where BioWare patched the scene to prevent it for a romanced Zevran).
If you want to include the possibility that a potential love interest from Book One might be open to flirting with a new Book Two protagonist, you might want to use event flags to prevent that from happening if that character was romanced in Book One. ie, if the Book Two main character has the option to flirt, the response can either be a positive reaction if the character is available, or a "Nah, sorry, not interested, I'm already seeing someone" if they were romanced (which can be a little squee moment for players happy that it implies their OTP is still together). Conversely, give the player even more power - when that option to flirt comes up, have a choice that reminds them that this NPC is already dating the Book One protagonist - and then give them the option to decide whether or not the two have broken up in the meantime (thus freeing the love interest for a new relationship), if the two are still together but in an open relationship where the new protagonist could also date them (thus freeing the love interest for a new relationship), or if the original protagonist wouldn't be okay with it (closing off the romance route for that NPC).
(For a humorous way to handle this, have flags for Book One gender and romance results, and when you get to that scene, have the original Book One protagonist pop in either in person or as a sort of fourth-wall breaking floating head, who points out "Hey, that's MY girlfriend!", and then have a choice that's like "...and I'm not cool with this. Go find your own love interest!", "...and I'm cool with sharing. Go you!", or "Woot! Orgy!")
The tl;dr for all this is basically that players love choice in games that promise them choice, and they want to feel like their choices matter. So any narrative decision that takes choice away from them (like telling them their main player character is okay with a relationship even if they aren't) is likely to annoy them, while giving them more power over the narrative (by letting them choose whether or not their character is okay with it) is likely to make them happy (or at least shut up most of the potential complainers).
That'd suck if both MCs were dudes, though.
