You need to make sure that the files on the device mounted by fuse will not have the same paths and file names as files which already existing in the nonempty mountpoint. Otherwise this would lead to confusion. If you are sure, pass -o nonempty to the mount command.
You can try what is happening using the following commands.. (Linux rocks!) .. without destroying anything..
// create 10 MB file
dd if=/dev/zero of=partition bs=1024 count=10240
// create loopdevice from that file
sudo losetup /dev/loop0 ./partition
// create filesystem on it
sudo e2mkfs.ext3 /dev/loop0
// mount the partition to temporary folder and create a file
mkdir test
sudo mount -o loop /dev/loop0 test
echo "bar" | sudo tee test/foo
# unmount the device
sudo umount /dev/loop0
# create the file again
echo "bar2" > test/foo
# now mount the device (having file with same name on it)
# and see what happens
sudo mount -o loop /dev/loop0 test