Armor Upgrades

[Ludens]

Does up-armoring a unit then make it susceptible to anti-armor units/missiles?

There seem to be a lot of misunderstanding about the AP bonus. The short answer to your question is: yes, units with AP abilities have an attack bonus against armoured units, but this bonus is never greater then the defence bonus conferred by the armour.

Now the long answer: the AP bonus is not a set bonus, but depends on the armour (inherent + upgrades, but not shield bonus) of the unit. Is calculated as [attack bonus] = ([target armour] - 1)/2, rounded DOWN.

So supposing you had a unit with armour = 2 and one armour upgrade (total armour = 2 + 1 = 3), the attack bonus for an AP unit will be (3 - 1)/2 = 1. The armour upgrade give the defending unit +1 defence, so these two cancel each other out. The armour upgrade has made your unit neither more nor less vulnerable to AP units. If you add another armour upgrade to it, the attack bonus for an AP unit will still be 1 [(4 - 1)/2 = 1.5 = 1], but your unit has +2 defence due to the armour upgrades, so your unit is actually better protected, even against AP units. If you add yet another armour upgrade (total armour = 2 + 3 = 5), the AP bonus becomes +2 against +3 defence by the extra armour. Adding the final armour upgrade (total armour = 2 + 4 = 6) gives +4 additional defence against +2 AP bonus to attack. So the unit will never be more vulnerable to AP units.
(Mind that this is just a example for a unit with an inherent armour of 2. If the inherent armour is different, the AP bonus kicks in at different levels of upgrade. Also, against cavalry the formula is slightly different, because a horse counts as +1 armour. The AP formula against cavalry is [attack bonus] = ([target armour] - 2)/2.)

Conclusion: whether an additional armour upgrade has an effect against an AP unit depends the exact armour levels of the defending unit, but it will never make your unit more vulnerable to AP units.

Now this is for melee AP units; ranged attacks work differently. Here too the game makes a comparison between the attack stat ('lethality') of the projectile and the armour stat of its target, provided, of course, that the projectile hits someone. Arrows from experienced archers are not more deadly, but they are more likely to hit. However, I do not know how the AP ability works for missiles. All I do know is that all missile weapons have an 'armour mod' stat. Non-AP weapons have a stat of 1, AP missiles have a stat between 1 and 0 and artillery has a stat of 0. My guess is that the armour of the unit is multiplied with the armour mod value before it is compared to the attack stat of the projectile, but whether there is a minimum threshold value like with the melee AP ability, and if and how it is rounded I do not know.