Chasidut zu Dewarim 25:3

The verse has thirteen Hebrew words. Through threefold repetition a total of thirty-nine words are recited. Perhaps this custom is an expression of the following thought. The sinner seemingly deserved forty lashes, but due to the Almighty’s compassion God looked deeply and acknowledged the voice of yechidah, and the sinner is only to receive thirty-nine blows.²¹⁷The scriptural source for the punishment of lashes contains a warning prohibiting excessive punishment. “He should be hit forty times, no more, lest you increase the amount of blows over these a great deal and your brother will then be embarrassed before you” (Deut. 25:3). Since the Rabbinic tradition revealed that the real limit is thirty-nine blows, the verse is referring to the fortieth blow, warning that forty blows is makkah rabbah, excessive. The gematria of makkah rabbah (65+207=272) is the same as the value of the words ve-hu rachum (18+254=272). This indicates that the compassion of God (represented by the words ve-hu rachum) is the reason for the liberal definition of makkah rabbah.
The Torah introduces the law of flogging with, im bin hakkos ha-rasha, “If the guilty party has incurred the penalty of lashes” (Deut. 25:2). The gematria of im bin hakkos ha-rasha (41+52+431+575=1099) is the same gematria as nefesh, ruach, neshamah, chayah, yechidah (430+214+395+23+37=1099). This is an indication of the lesson mentioned above. At the moment of flogging all the parts of the soul appear, the blows are then reduced, since the pure yechidah is present (Emunas Etecha, 5757, pg. 7).