She realized she didn’t have a legal leg to stand on and didn’t want to be royally smacked down by the Supreme Court who has for 230+ years ruled the presidential pardon power is dang near absolute.
President Trump issued his pardon after a motion had already been filed by Arpaio's legal team to have his original conviction overturned. Arpaio could have just dropped the whole thing at that point, but there was apparently some legal technicality in play that motivated him and his lawyers to insist that the judge consider the motion anyway. I believe it had something to do with the way Arpaio's legal record would be documented if he ever needed a security clearance in the future (or something like that).
For whatever reason, Arpaio and his lawyers decided that having his original conviction overturned was preferable to having the charges disappear through the pardon.
The judge was never going to overturn Arpaio's pardon under any circumstances.
“She realized she didn’t have a legal leg to stand on and didn’t want to be royally smacked down by the Supreme Court who has for 230+ years ruled the presidential pardon power is dang near absolute.”
Forget the SCOTUS, this Judge might have lost her job due to un-Constitutional behavior, and I suspect that the local judicial circuit received more than one ethics complaint about her.