What is the halacha if I checked an esrog and it is perfectly fine and then decide to get a closer look with a magnifying glass and see that this esrog has a pasul. Do we say its passul now since we see a problem even though the Torah doesnt require a magnifying glass,or do we say that the Torah does not require us to use a magnifying glass and a deficiency so small doesnt count unless it can be seen without assistance ?
R Hadar Margolin (in The lulav and esrog handbook, p. 35) answers this question
Since these disqualifications are based on what people see, the spot must be clearly visible. Thus, if the spot is so tiny that it cannot be seen by the unaided eye without great scrutiny, it does not disqualify the etrog (Mishnah Brura [648:]46).
The accepted definition of "not visible without scrutiny" is a spot that is not visible when held as far away from the eye as an etrog is normally held (Mabit III:49, Graz 648:22, Pri Megadim, Eishel Avraham sv ketzas dinei etrog, Shaar HaTziyun 648:49).
Needless to say, a spot that can only be detected under a magnifying glass does not affect the acceptability or the hiddur (beauty) of an etrog
In summary, the etrog is, for now, as good as without the blemish. But remember to ask your local rav should this happen in real life.
The Mishna Brurah (648 s.k. 46) states:
ודוקא כשנראה לכל אבל אם אין נראה לעין מחמת דקותו וצריך להסתכל אין זה כל שהוא שפוסל
It is only [disqualified] when it is visible to all, but if it is not visible to the naked eye due to its small size and one would need to look very carefully [because he would otherwise not see it], this is not a disqualifying blemish.
It should be noted that the Mishna Brurah is discussing a case in which the blemish is not visible at all without close inspection. However, if the blemish is visible albeit very small, and one needs to examine closely (with a magnifying glass) to determine if the dot he sees is a disqualifying blemish, that could potentially be posel.
I found that Chacham Ovadia discusses this in Yechaveh Daas 6:47, he is talking about worms in water but also discusses other items in the teshuva.
He brings from Rav Yosef Messas Mayim Chaim siman 259 which says that an esrog that has holes in it, but those holes can only be seen with a magnifying glass, then the esrog is considered kosher even l'mehadrin, since we only qualify the esrog based on one's eyesight without any outside assistance (enhancers).