Does FMLA guarantee a comparable shift?

What is the name of your state? Colorado

One of my exempt employees has been on a continuous leave of absence since mid-June. Part of her leave was covered under FMLA, but exhausted available time months ago. While she is on leave, does the law require us to allow her to participate in shift bids? Does she have a right to pick her shift upon return? At what point does one lose their seniority?

The first day her FMLA was exhausted, she lost her guaranteed rights to reinstatement, let alone a comparable shift.

If she had returned to work within or immediately following her FMLA, she would have to be returned to either her old position or one that was comparable in all respects, including shift. However, since her FMLA has been exhausted, you don't even have to return her to work, let alone to the same shift or position.

BTW, even FMLA does not protect her from any action that would have taken place regardless of whether she took leave or not.