It IS possible that the only thing wrong with this ASF was that it was born a bit small, and failed to compete for milk effectively with its numerous siblings. It may have appeared malnourished simply because it was--if it's begun to recover, develop and grow after being placed with a smaller litter, it may be because now it is getting sufficient milk. (Just because it's nursing doesn't mean it's getting sufficient milk--if mom has none left, then baby gets none).

The animal may make a 100% full recovery, and its issues may have been due to nothing other than the bad luck of being born a bit weak in a litter that was too large.

Malnutrition can cause many physical issues--the eye issue and other signs may have been due to absolutely nothing other than that, particularly since they're now going away. There may be no genetic abnormalities at all.

I'm personally not all that sentimental, and would feed it off once it's reached sufficient size. The sturdiest, strongest, fastest growing, and most docile animals should be used for breeders, after all.