In SimPE, I ran Sim Surgery to give the Patient Sim (Sim A) with deleted CC eyes the same eye color as the Archetype Sim (Sim B) (and checkmarked Eyes only), but it didn't work.

So what are alternative methods to swap the missing eye color of Sim A with the exisisting eye color of Sim B on a genetic level?

You fix a sim with missing eyes by opening their character file in two areas.

So you want the MORE section down the far right, open that and you will see a DNA section. Then you need to know the code for the eyes that you want. Maxis eyes are the easiest as those codes are known, so if the sim is going to use default eyes you simply put in the Maxis code in the relevant area. You can do both dominant and a receive eye code.
Brown: 32dee745-b6ce-419f-9e86-ae93802d2682
Dark Blue: 2d6839c5-0b7c-48a1-9c55-4bd9cc873b0f
Green: 51c4a750-c9f4-4cfe-801c-898efc360cb7
Light Blue: e43f3360-3a08-4755-8b83-a0d37a6c424b
Grey: 0758508c-7111-40f9-b33b-706464626ac9
Alien: 12d4f3e1-fdbe-4fe7-ace3-46dd9ff52b51

Make sure to commit.

Then you open the MORE> Open Character File area and go to Age Data where you will find eye colour, that also needs the eye code. Commit and save.

Load up your household and send the sim to a mirror to update their appearance. Eyes should be fixed and this is genetic.

If you want an eye that isn't a default you will need to open a sim with that eye and copy paste the code from them to use.
Or open the eye file itself and go to Texture Overlay XML (XTOL) resource and copy the value in the “family(dString)”