Well, I'm going to rock the boat a little bit, and leave rather a long answer to the o/q:
A combatant enters a area--be it a square, a hex, or space on the table where their bases would be in contact were both figures "on table"--where another combatant is present but concealed.
How does one resolve that in a Pathfinder game, by rule?
My solution is to allow the Inactive Combatant to decide whether to maintain concealment, or to engage. Engagement forces the Active Combatant to move back to the immediately vacated space, and permits the usual melee rules to be employed thereafter.
Maintaining concealment requires the Inactive Combatant to take a 5' Step to an adjacent space as an Immediate Action, and make some sort of GM-set Stealth Check; unless the GM frequently has Players make Perception/Stealth Checks during melee movement, making an opposed check gives the game away and negates the intent of the Inactive Combatant. If the Inactive Combatant succeeds in their Stealth Check, they remain concealed (Invisible) and retain the ability to act on their Initiative Turn. If they miss their Stealth Check, they are pushed 5' along the direction of movement of the Active Combatant, and are engaged.
Here's why...
My foundational premise is to remember that rules conflicts occur during game play, and therefore, my role as GM is to adjudicate them within the scope of the current game situation. The fundamental consideration for me as a GM is therefore intent. Determining intent isn't as vague or notional as it might appear, because game situations inform intent rather nicely.
The Active Combatant and the Inactive Combatant both have an intention, made evident by their preceding Actions and their own declarations. In the original situation, the Active Combatant--the Drow--is moving towards a destination; they are not simply wandering about, nor are they specifically searching for concealed combatants. The Active Combatant's intent is to Move from 'A' to 'B'.
The Inactive Combatant--the Invisible Ninja--is employing concealment (Invisibility) for a reason which is unfortunately not illuminated in the OQ. Whatever the Invisible Ninja ultimately means to do--make a Sneak Attack, slip away unnoticed, or simply observe the other combatants--it is reasonable to presume from the information provided that maintaining their concealment (Invisibility) is their paramount concern.
The Active Combatant has an objective, and their objective is not to discover an Invisible Ninja they have no idea is present. On the other hand, the Inactive Combatant's objective is to to remain concealed (Invisible), and they can clearly observe the approach of the Active Combatant.
I want to preserve the intent of both combatants, where I can. Certainly the rules--even the RAW--support me in that effort, even if they can always be read so as to support a different conclusion by some one determined to create disharmony.
My first decision is that leaving both combatants in the same rea is clearly a poor choice, because the Minimum Space Abstraction (a 5'x5' square) was chosen as the area occupied by one person-sized (Medium) combatant. It is explicitly forbidden by rule, as well.
So how might one employ the rules to adjudicate this general situation?
Firstly, it is clearly considered possible for two combatants to move in close proximity to one another in Pathfinder, because Friendly combatants are able to move through the Minimum Space Abstraction (a 5'x5' square) without jostling each other, slowing one another down, &c; they just glide by. The rule is so broad that the main exception is singled out: a Friendly combatant cannot Charge through an ally's space.
So...it seems reasonable to assert that a Neutral or Enemy Inactive Combatant could manage the task of avoiding an enemy combatant as they move through the space they occupy, at some cost and some risk of detection. The Invisible Ninja is likely to be particularly good at this, but at the moment, I want to focus on the general case, rather than specifics.
Secondly, an Inactive Combatant who is visible is permitted to simply step away from an Overrun attempt, which is really the best the Active Combatant could assert as their privilege in this situation; they don't know the Inactive Combatant is in front of them, after all.
So...it seems reasonable to assert that a combatant is permitted to Move the minimum distance abstraction (a 5' Step) in order to avoid an Opponent, as well as manoeuvering to allow an Ally to pass through their space.
Thirdly, a Reflex Saving Throw is an attempt to manoeuver out of the way of an attack or effect.
Fourthly, the Action Economy is rife with examples of Inactive Combatants being permitted to "do things" which are "quasi Actions" as a reaction to activity and events around them. Fleeing is an obvious example.
So, it is clearly understood that the Action Economy's poor synchronisation to the abstraction of Initiative Order requires a major investment in rules exceptions, This further supports an asynchronous resolution of the situation.
Given the Active Combatant is not deliberately seeking to find concealed foes, that Inactive Combatants--even without a Readied Action--are permitted to react to events, and that the most similar melee situation permits the target to evade by making an asynchronous Movement of 5', the resolution is fairly clear:
The Inactive Combatant must decide to either maintain concealment, or to engage. Engagement forces the Active Combatant to move back to the immediately vacated space, and permits the usual melee rules to be employed thereafter. To maintain concealment, the Inactive Combatant must take a 5' Step to an adjacent space as an Immediate Action, and make some sort of secret Stealth Check; unless the GM frequently has Players make Perception/Stealth checks during movement, making an opposed check gives the game away and negates the intent of the Inactive Combatant. If the Inactive Combatant succeeds in their Stealth Check (against a GM-set Difficulty), they remain concealed (Invisible) and retain the ability to act on their Initiative Turn.
The GM might charge the Inactive Combatant a Move Action, or charge off an Opportunity Attack, or find some other way to kludge together the nightmare that is Actions in D20 FRPGs. The OQ had the Inactive Combatant charged 5' of Movement.
The real issue, of course, is the ugliness that is the D20 Action Economy, whether in V1 or V2.
KAH