Typical Theater
The article about this yesterday mentioned that three disks were used to load a control program onto a MS-DOS based system, the control system maintaining safe spacing of MUNI trams inside the tunnel. This system is to be replaced by a Hitachi train control system controlling the entire network at the bargain (?) price of $200 million plus.
Replacing a floppy drive is a no-brainer. It might be a bit fiddly in a very old MS-DOS based system because of the lack of USB support but this is San Francisco, right?** There should be no shortage of local talent to figure this out. MS-DOS might be a bit old but its only acting as a loader and at least we know that its bug-free. I suppose sales people couldn't conceive of a Raspberry Pi Zero control system (equal to half a dozen or more vintage PCs), they have to get something that's over designed -- and likely overpriced -- for the job.
(**An interim solution that would be really easy to implement would be to replace the 5.25" drive with a 3.5" one. It will just plug in. One of these disks will carry the three disks' worth of data.)