Filesystem refresh/reload

Hi, I'm developing an OS out of assembly, Casnix (http://casnix.sourceforge.net).

I do most of the development with cygwin, on my usb flash drive. But when I write to the disk image, I need a linux machine for the loopback device from the kernel.

Earlier, I had to rebuild the kernel because the kernel source folder was corrupted, but when I mounted my usb on my linux machine (Damn Small Linux), I can't see the new files, nor does linux see them.

Cygwin:

$ ls

kernel.asm //new

kernel.bin //new

caswellboot.bin //new

casnix-1.0.1.flp //old

kernel/

programs/

docs/

boot/

after_compile/

On DSL:

$ ls

casnix-1.0.1.flp

kernel/

programs/

docs/

boot/

after_compile/

How do I refresh the filesystem without loosing time by rebooting my machine?

I don't know if this post makes sense, and I'm assuming it's a software problem.