If the man is judged to only be able to take any number under 39 ie. 12 mackos, but before they could give the punishment the aydim that first said aydus against him were found to be zomimin do the aydus get 39 or 12 mackos?
Your question is posed by the TIFERES YAKOV (Mishnayos Makos, 3:70). Although he does not resolve it, it would seem clear that even if the Malkus for Edim Zomemim is because of "Ka'asher Zamam" and not "Lo Sa'aneh" (see Rambam Hilchos Sanhedrin 20:2, and Acharonim), they still would get 39 Malkus each if they are able to survive that many.
The reason for this is twofold. Malkus is a single punishment, which expresses itself differently depending on the strength of the person who is sustaining them. Therefore we can give the witnesses 39 Malkus.There is not such thing as less than 39 Malkus for a person who can sustain that many. It would not be Ka'asher Zamam to give less. (The TZAFNAS PANE'ACH proposes this argument, basing his words in part on Rashi Kerisus 11a DH b'Vikores).
In addition, there is no way for the witnesses to determine what Beis Din (and their doctors) will decide regarding the man's physical strength. They may think he can sustain more Makos than the witnesses think, and even if the man is very obviously weak he may regain his strength before the Omed. Since it is out of their hands, and before the Gemar Din the Beis Din has not actually made an Omed, it is as if the witnesses were ready to give the defendant the full 39 Malkus.