There are several things going on
(1) Files added with
--raw-leaves so you need to specify in order to get the same hash when adding files without the
(2) You might need to reverse the order, that is first the file with
--raw-leaves --nocopy then with just
(3) Due to what is probably a bug, it seams ipfs will not complain if a file can not be added via the filestore due to path restrictions and instead add it normally.