If you regularly back up your BeOS system with zip, BeB, or anything else, why not back up your Windows data in the same session? Since BeOS can read FAT volumes just fine, you can make it all part of the same backup procedure.
If you do it with zip, your backups will even be readable from within Windows. If you’re scripting your backups, you’ll probably want to create separate archives from within the script — one for your BeOS data and another for Windows data, just so you can move the Windows archive over and deal with it separately if necessary.
And if you’re also using the Linux filesystem driver, there’s no reason you shouldn’t be able to back up all three operating systems from within BeOS.