I think here's the thing.
Technically speaking, within a US district, only the United States Attorney or an attorney specifically authorized by the AG under 28 USC 515 to bring charges (a "special attorney"), is authorized to indict.
Assistant US Attorneys act in the name of the US Attorney.
So if there is no validly serving/appointed US Attorney or special attorney, valid indictments may not be brought in that District.
I think if you look at other indictments across the board, you'll see a signature block that is:
___________________________
United States Attorney for ____________ District
by _________________________
Assistant United States Attorney
If the US Attorney doesn't sign his or her self.
So, they're having the conundrum that dipshits worldwide have when they fuck up. Should they pretend Halligan is the validly appointed/serving US Attorney and fuck up other indictments, or does appointing someone else unfuck future indictments but undercut the notion that Halligan is validly serving.