No, I'm sure there were other clean underpants in her drawer. They were chosen because 1) they were the same type that she had worn that day, and the same day of the week. A male wouldn't have known that and if it were pointed out, he'd likely have said it didn't matter. Patsy *would* know, and might feel in the moment like the cleanest option (brand new) was a pair of panties that were ostensibly the same, but it turned out they were far too huge for JonBenet so not believable that she wore them herself all day. Ironically, whoever changed her into those underpants really undermined their intruder story, because how would an intruder have found another pair of underwear to dress her in? And why would he have bothered?
If it was Patsy who decided to use those panties, she wasn't thinking clearly or she was thinking that someone knew what underwear JonBenet had worn that day and if it were another pair, that someone might find out and use it to prosecute the family. If it wasn't Patsy, the person who did it wanted JBR to be found in those too-huge underpants for other reasons.