A resource file can be archived without breaking the file hierarchy that CKAN builds under /var/lib/files/resources. The actual data for a resource 7896ea0c-504d-401c-818f-065430419695 will be stored as a regular file under a 3-level hierarchy at 789/6ea/0c-504d-401c-818f-065430419695.
For example:
tree resources
...