I can confirm this happens with vehicles. I found out that the part that depends on the total damage will get reset because Total can only be reset using setDamage.

Example:

Using the RHS MI24P, set damage using "setDamage 0.6"; observe every hitpoint set to 0.6, as in the steps to reproduce.

Follow the rest of the reproduction steps and end up with all hit point damages set to 0.

Enter the vehicle and observe all components are shown as white; start up the engine and the hull immediately turns red/orange. (dependent on the original setDamage value)

Check the getHitPointDamage for "hithull", see it has magically reverted to 0.6 because "Total" can't be changed using hitpoint and is not even a hitpoint.

The only possible fix I see is to make it so that if "hithull" (or whichever hitpoint depends on "Total") gets set, "Total" gets set.

Heya @NeilZar ! :)
This should only be valid for helicopters - their hitHull HPs are configured with depends = "Total". (May be true for some other or modded vehicles too)
If I do

vehicle player setDamage 0.6;
{vehicle player setHitIndex [_ForEachIndex,0];} forEach ((getAllHitpointsDamage vehicle player) select 0)

on a vanilla tank the hitHull remains 0.0.

Thanks for the reply @oukej

I didn't notice the issue with tanks, indeed. It is still annoying to have to do _vehicle setDamage 0 after having set all hitpoints to 0 on a helicopter.

Is there a reason why only helicopters have the hithull hp depend on the Total hp?

I am sorry to say we won't be changing the behavior. When altering the damage with script it's needed to take care about both - the HPs and Total damage (or even take the affected vehicle config into account).
We can't change the behavior without affecting already released content and there might be situations when you want to just change one HP without affecting the Total damage.

@NeilZar Is there a reason why only helicopters have the hithull hp depend on the Total hp? Most probably a legacy thing :/ After the tank damage improvements it would be nice to also take a look at how our other vehicles (e.g. aerial...) were set up, but I'm this will remain only as a wish.

Yea, that would probably be against the current stance of no more engine changes so mods don't get broken every time.