Salmon Trout's method works. I wasn't familiar with it so I just gave it a shot in VMWare under MS-DOS 6.22.
The VM I have only has one floppy drive. I was able to use chkdsk on a bootable floppy image and run it against a separate image that had only data files using the "Phantom drive" approach.
A simple "scandisk B:" when A: is the current drive seemed to do the trick. It prompted for the disk for B:, and I swapped in the data diskette.
LKooks like you can also change to the data diskette directly via B: and then run A:\scandisk B: and it prompts for the A: diskette, then the B: Diskette, and the program runs against B:.