Suppose a medium-sized Eidolon has spent 2 evolution points for the Ability Increase (Strength) evolution. Later, the Summoner gains a level and gives the Eidolon the Large evolution.

According to the Large evolution,

The ability increase evolution costs twice as much (4 evolution points) when adding to the Strength or Constitution scores of a Large or Huge eidolon.

Additionally, by the RAW reading of the Summoner's Eidolon class feature, their evolution points are reallocated each level.

Whenever the summoner gains a level, he must decide how these points are spent, and they are set until he gains another level of summoner.

When the Eidolon gains the Large evolution, does this retroactively increase the cost of the already-purchased Ability Increase evolution (from 2 points to 4 points)? Or does this only increase the cost of future purchases of the Ability Increase evolution, such as through the evolution surge spell?

A summoner spends all evolution points at each new class level

The summoner on Eidolon, in part, says

In addition, each eidolon receives a pool of evolution points, based on the summoner’s class level, that can be used to give the eidolon different abilities and powers. Whenever the summoner gains a level, he must decide how these points are spent, and they are set until he gains another level of summoner.

As can be seen in the section Eidolon on Table: Eidolon Base Statistics, evolution points aren't additive. For example, the Evolution Pool column does not start at 3 points at level 1 then say +1 at level 2. Instead, the Evolution Pool column goes from 3 at level 1 to 4 at level 2.

Thus, at each new summoner level, the summoner first removes from the eidolon all the evolution points that the summoner spent the previous level then spends the current level's evolution points. The summoner may end up spending those evolution points in almost exactly the same way as the summoner did the previous level, but that doesn't mean that the eidolon keeps the previous level's evolutions and the summoner's only, like, spends the difference. Instead, it just means that at the new level the summoner's made choices similar to those the summoner made the previous level.

For example, at level 1 a typical eidolon has 3 evolution points that the summoner picks how to spend. Then, when the summoner advances to level 2, a typical eidolon has 4 evolution points that the summoner picks how to spend. However, a summoner can't opt only to spend 1 evolution point—the difference between the eidolon's evolution points at summoner level 1 and its evolution points at summoner level 2—so as to leave the remainder of the evolution points still spent as-is. The summoner must first flush out all of the evolution points that were spent at level 1, and then the summoner can spend the evolution points available at level 2—even if that means the summoner spends the evolution points in almost exactly the same way as they were spent at the previous level.

So if a summoner's eidolon has the evolution ability increase, and the summoner gains a level, the summoner purges from the eidolon all its evolutions, including the evolution ability increase. Then if the summoner buys with the current level's evolution points the evolution large so as to make the eidolon Huge and the summoner wants to buy the evolution ability increase, the summoner'll have to pay 4 points instead of 2 if the ability increase evolution is to affect the eidolon's Strength of Constitution scores.

The summoner isn't, like, rewarded for his foresight for picking the evolution ability increase for a littler eidolon then keeping that evolution until the eidolon's size is Huge. Instead, the summoner is forced by the rules quoted above to purchase anew every level that he wants the eidolon to have it the evolution ability increase, and if he does so when he's also made his eidolon Huge via the large evolution and picks the ability increase to apply to the eidolon's Strength or Constitution, then the ability increase evolution costs 4 evolution points instead of 2 evolution points.

Everything is recalculated on level up

No, it doesn't retroactively increase it, you are effectively creating a new eidolon every time level up as a summoner:

Whenever the summoner gains a level, he must decide how these points are spent, and they are set until he gains another level of summoner.

Not only that, but since they are treated as summoned creatures, you are effectively summoning a new creature every time your eidolon is summoned:

The eidolon forms a link with the summoner, who, forever after, summons an aspect of the same creature. (...) Eidolons are treated as summoned creatures, except (...)

As noted by James Jacobs (Paizo's Creative Director):

It summons a "copy" of an idealized incarnation of the creature. A summoned creature doesn't exist before you cast the spell, nor does it exist once the spell expires.

That's the difference between summoning spells and calling spells. Calling spells DO conjure a real creature.

On evolution surge

James Jacobs has clarified that you may add the Large evolution normally to an eidolon that already possesses ability score increases, stacking those bonuses as they are all untyped:

Evolution surge doesn't make you lose existing evolutions. It gives you a new one. When you cast evolution surge on an eidolon to grant it the Large evolution, it gains untyped bonuses to its ability scores. Likewise, the Ability Increase evolution (I assume this is what you're talking about with the "Ability boost Strength evolution") grants untyped bonuses. As a result, they add together and stack; your eidolon would gain a net +12 to its Strength score.