Is it possible to use an existing folder in the filesystem as the
"target" directory for an iFolder? So that, e.g., when syncing for the
first time, the client could find the differences between the two
folders and only download the missing/different files (if any)?

The main reason I'm asking is that I have a dual-boot system with a
shared FAT32 partition where I want to have an iFolder. But I'd want
to be able to sync to this iFolder from either OS, and I'm not sure how
to go about that or if it's even possible.

If I were to convert the folder to an iFolder in one OS, sync it to the
server, then boot into the other OS, delete the original folder, and
download the iFolder to the same location, would this achieve the same
thing (other than having to needlessly re-download the whole folder,
which is a bit of a hassle)? Or would I run into some complications
that I'm not thinking of?