Control his information.
If his reloading is conscious (he decides to do it) then you can try to control his information. With an unlimited budget, you basically create an environment for him that works like the Truman Show: a potempkin village where the people around him are actors, his phone and computer are 100% hacked and displaying information you want him to have, and wherever he goes, he sees what you want him to see or is prevented from going there (not captured: prevented).
If his reloading is unconscious, you may have more options. You experiment with him until you know what constitutes "capture" and then you herd him to a place or locale where he isn't technically "captured" -there was no real "moment of capture" because he was traveling -something like the bottom of the Grand Canyon. You seal the exits and leave him be. You might experiment with this reloading as it applies to speed of death. In other words: if he starves to death over the course of several weeks, does it reload to before those weeks? If so, you can just throw him enough food to keep him alive but neutralized.
If none of the above works, you have to analyze HOW he is causing you trouble and deal with that. If he is causing trouble because he gets information out, you block his ability to do that, but otherwise leave him unharmed and un-captured. If he is planting bombs, you follow him constantly and diffuse the bombs, but leave him alone, prevent him from buying materials, etc. You follow him constantly, tail him everywhere he goes, and just stop him from doing specific things in ways that do NOT trigger a "reload".