: How to balance the agendas of co protagonists that periodically conflict? While not mutually exclusive, the goals of my co protagonists do conflict and I need to keep them balanced. MC1 works

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Hide their goals.

You are writing about professionals. They would be less than amateurs in their line of business if they were to reveal their goal so easily. In fact, revealing one's goal gives the other leverage to achieve theirs.

Instead, structure their goals like an onion. Layer after layer of misleading goals. A pile of seemingly righteous objectives, which they will strive to achieve, but that mean nothing to your characters.

These fake objectives can be negotiated (creating conflict), and surrendered (resolving conflict, advancing the plot) if needed, but not without giving the impression that was really their true goal. Let them reveal that their "real goal" is in fact , while, in fact, it is just another ploy.

Of course, these alternative goals have to somehow be related to the global intended goal, else they may completely derail their overall mission. E.g. if they need to uncover a mole in the organization, the fake goal should not really be "resigning to grow tomatoes in the garden", but rather "hiring a new trustworthy member" or "getting in touch with foreign agency".

In this way, the agendas of your characters are fairly balanced. They will try to:

achieve their global goal
pretend to be achieving their fake goal
put obstacles against the fake goal of the other character in order to gain leverage
try to second guess the true goal of the other character, and putting obstacles against that as well

Of course, your readers will have no clue until the end, and just revere these two masterminds outsmart one another.

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How best to keep these occasionally polarizing aims balanced without
creating reader whiplash?

This is character conflict and it's a good thing

I think it's not about which character is "winning" at any given moment, but about this trust dynamic between the characters.

Over the course of the plot, each character will need to negotiate their own level of habitual nature, short-term goals, and long-term goals. There's something they want/need in both the short term and the long which makes them willing to form short and long-term alliances, but there's also something that triggers them – a personal breaking point.

Story-wise, the breaking point won't be an accumulation of circumstances, it will be a specific thing that "breaks the suspension of animosity". It's a specific story beat, which is probably built up to or repeated as a pattern. The character can put up with a lot, but this one thing is a line that when crossed, the alliance is over. The characters won't telegraph it to each other – they will keep their game faces – but the reader should pick up when that line has been crossed. The sub-text changes, or the character begins to act with suspicion or caution.

This dynamic has it's own arc that you can roughly pace against the timeline of events. It might look something like:

Enemy agents, anonymous distrust
Personal encounter, direct animosity (They shoot at each other.)
calculated negotiation (surrender and you will live.) long-term/short-term compromise
long-term goal, and anonymous trust (As a members of law enforcement, we have reasons to work together.)
long-term goal, personal trust (Working together, seeing the other is competent)
long-term goal, but a trigger leads to personal mistrust (trust erodes)
short term compromise (work together for now, but look for exit strategy)
Other character's trigger (the discovery of an exit strategy undermines trust in both long and short term goals)

You are moving the trust "needle" through the various stages. Build trust with shared long and short term goals, break trust with triggers but negotiate with long vs short term goals.

The characters won't act until an opportunity arrives, and they won't telegraph their trust level to the other characters ahead of being able to do something about it. Use this shifting trust dynamic to justify the twists in the plot, not the other way around. Signal the trust level ahead of plot twists and sudden character turns. The reader won't get whiplash, the story will start to make sense because the character's behavior is consistent with their goals and triggers.

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Your characters are in a situation that reminds me of a programming problem. I'm referring to the Race Condition between two threads problem.
Briefly, a race condition happens if two parallel execution threads attempt to manipulate a common resource. A typical solution for this is to create what is called critical section surrounding the common resource. So, the first thread that obtains control over the critical section, will lock the resource for others until it frees it.
You could treat your MCs' plots as threads. Since you wrote in a comment that their common goal is survival; make the survival of MC1 depend on MC2, and have the latter absolutely control the survival of the former. This control is your critical section.
Rasdashan wrote in comments:

...if I have MC2 keep MC1 under her thumb, he remains a prisoner and his duty is to escape - which would logically occur when least convenient to her. She needs his loyalty - even short term - to render him an ally rather than a prisoner.
...
That conflict was always there, but how to preserve the balance between the two occasionally opposing goals of these two who have been set together yet in opposition.

You could preserve the balance by bouncing the "ball" between the two characters. In other words, give control of the critical section to the opposing side alternatively until you find the pace you are looking for.

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