1) I have several people checking running their POP accounts through my POPfile system. Can they still do that on windows, and with the same syntax?

Yes.
The users just need to change their account configurations.

2) How do I migrate the corpus and configuration from Linux to Windows?

1. Backup the database (popfile.db) and the configuration file (popfile.cfg).
2. Install POPFile on your Windows machine.
3. Stop POPFile
4. Copy the back files that you backed up at the first step to the POPFile data folder.
5. Restart POPFile

For more information, see:

http://getpopfile.org/docs/howtos:backup

Please note that the Windows version has some limitations.
You can see some of them in our release notes:

http://getpopfile.org/docs/releasenotes:1.0.1

If you are sharing POPFile with many users, I personally
don't recommend you use the Windows version.

Naoki