you could do it like this:
-----------------------------
example upload (examples for cp/sync): #did it with if else, because I find it easiest to explain with mount it should be same but adapted
if (does directory already have a directory file?)
	else{
		create directory file
		}
if (is there an entry in source directory file?)
	else{
		if(is file local?)
			{
			create hash and add it to the directory
			}

			else{
				download
				create and add hash
				}
		}
Upload file
download file
create hash of the downloaded file
if (hash == as in directory file)
	else{
		jump to file upload. compare again until file == hash or it failed 3 times
		}
if (all files uploaded from the directory file?)
	{
	upload local file with all hash also encrypted and check again, same as above
	}
	else
		{
		back to the beginning
		}
upload next directory and start again from the top
-----------------------------
example download (examples for cp/sync):
if (is a directory being downloaded?)
	{
	x=1
	}
	else
		{
		x=0
		}
if (x=0)
	{
	download file
	hash create
	if (hash == as in remote directory file) #download directory file only temporarily to get the hash
	else{
		jump to file download and compare again until file == hash or it failed 3 times
		}
else
	{
	download directory file
	y=0
	while (y != z) #z number of files in directory
		{
		y download #y the file which is currently in the sequence starting with 0
		hash create
		if (hash == hash from local directory file) #download directory file only temporarily to get the hash
		else{
			jump to file download and compare again until file == hash or it failed 3 times
			}
		y += 1
		}
	if (all files downloaded from the directory?)
		{y=0}
		else
			{
			back to the beginning
			}
	next directory and start from top
	}
-----------------------------
the directory file could then be written as a hidden file so that it is synchronized with, but has a unique name and is not easily visible. but so that it can be found.

my head is throbbing... hope I haven't forgotten anything and no I am not a programmer :D

hope I didn't forget anything when yes, than just ask :)