The Yerushalmi [Bava Kamma 3-4] says that the first time the בן סורר ומורה steals he is not פטור from כפל [unless we say that the first time he steals is also part of what is ultimately מחייב him מיתה in which case he wouldn't have to pay the monetary obligation - see there].

Asked the Acharonim: The מלקות that he gets for the גניבה should at least absolve him from the חיוב כפל? He can't get two punishments so it should just be the מלקות?! Numerous answers have been offered to this question.

We can answer based on Rashi [Sanhedrin 71a]. The mishna says that the parents give the בן סו"מ a התראה. Rashi explains that this is not a typical התראה given before someone sins. He proves this from the fact that for התראה we need kosher witnesses and his parents don't fit the bill. Also, the התראה must be issued immediately before the offense but here the parents warn him well in advance and then he goes behind their backs and steals and gorges. So here Rashi says that it is an admonishment but not a typical התראה. 

It would seem that not only is the התראה atypical but the מלקות that he is given are also atypical. We make this assertion based on the fact that the התראה and the מלקות are derived from the same pasuk ["ויסרו אותו"]. So just as the התראה is unique, so too are the מלקות. For this very reason we don't require התראה for these מלקות because these are not typical מלקות but rather an admonishment. 

That would also explain the Yerushalmi which understood that there is no פטור from כפל because of these מלקות. Since they are not coming as a typical punishment, they don't fall under the rubric of

 "כדי רשעתו - משום רשעה אחת אתה מחייבו ואי אתה מחייבו משום שתי רשעיות"      

We can only give one punishment and not two. That applies only to מלקות given as a punishment but not to these special מלקות given as admonishment. 

With this we can answer the question of the Haflaah [.ל"ה] who asks about the gemara [Sanhedrin 74a] which says that a רודף doesn't absolve the נרדף from having to pay ממון if he could prevent his sin by harming but not killing him - להציל באחד מאבריו. Since there is no need to kill him, the ממון remains obligatory. Asked the Haflaah: Why don't we say that he is פטור because the רודף may harm him? Why is this different from any punishment of מלקות that makes one פטור from ממון?

Based on the foregoing we can answer this question. Not every bodily punishment is included in "כדי רשעתו" as we illustrated, that sometimes even מלקות themselves aren't typical מלקות and don't count as punishment to absolve from monetary payment. Here too, the דין of להציל מאחד מאבריו doesn't count as punishment to absolve from ממון.