Not A Lawyer
Somewhere there is a thread which mentions a story about a guy who was either charges, convicted, or lost a civil case (can't remember which), because the reloads he had performed differently than similar factory ammo that a lab tech tested, resulting in the lab tech coming to an erronious conclusion about the range or angle at which the shot was fired. It was not the fact that they were reloads per se, but only that the real round used in the shooting performed differently from the round tested by the lab. It was a lab screw up. That's the only case I remember specifically named where reloads mattered at all. I never looked up the case, so I don't know if the description in the retelling was accurate.
I can tell you that I have seen lawyers make every arguement udner the sun, and sometimes someone (the judge, the juror, just one juror, etc.) buys it and sometimes they don't. There are enough theories about using reloads being brought up in court that eventually a DA will read one of those theories, get a shooting involving reloads, and make the argument, if it hasn't happened already. It's a really good arguement to use, especially in front of a jury that may have shooters and sportsmen cleared out of it.
Will it make all the difference in a case, where it turns a 100% justified shooting into a pre-meditated murder conviction? I'd say it COULD, only because I've seen cases where jurors get hung up on one piece of evidence, or one statement, including something they misheard or don't remember correctly. I could definantely see a case where a DA says "I'm telling you that Joe Smith loaded his own super bullets to make sure the victim would die", and a juror hears, "Joe Smith said [or told someone] that he loaded his own super bullets to make sure that the victim would die". It doesn't happen in every case, but that kind of thing happens. All in all, I would suspect that it is very unlikely to turn a case from "not guilty" to "guilty". I would also bet that it is VERY UNLIKELY to be the deciding factor in whether the DA prosecutes the case. It's not impossible, and I'd hate to be the guy who gets hit with it, but I don't think I'd lose sleep over it.
Now, if you had somekind of weird ammunition, like poisoned bullets, exploding bullets, a bullet with a homemade penetrator, or something, that would be a different story, and could cause the police, DA, or jury to take an extra look at what happened, and take a negative view of you as the shooter. A poisoned bullet, for example, could turn a justified shooting into a murder, because the poisoned bullet is "unreasonable".
My biggest worry with a reload is that they wouldn't work right.