There are files in your appdata folder called usb#{giantstringofnumbersandletters}.MBL that, I believe, tell MB which files are on your phone.
If you really want to be able to sync from different machines and have it be the same, you'd probably have to run portable MB on a network share as well and open that same copy on each of the PCs. I do this, and it works, although it takes some thinking-through to set up. I don't know if even that would work, though, because the USB address for the phone would be different between the machines.
Personally I just have one computer I sync from because why unduly complicate things that I've already complicated enough with my complex setup? But that's just me.