Look in moodle data folder/temp/backup/ of the 2 instance.
One should find 0 byte 'hash-named' dot log files of restores that were successful and (possibly) 'hash-named' dot log files with more than 0 bytes of restores that failed - as well as 'hash-named' files/folders which one can 'browse'. Those might give you some hints.
Suggest making a copy of the 1.9 course ON the 1.9 system and changing some basic information ... maybe even re-naming files contained therein - all lower case no spaces or 'special characters', all have extensions that are lower case, etc. One could do that using the Files link in the course admin menu. Be sure to re-link to those files in the course.
Did the course in the 1.9 contain any blocks/mods (resources) that aren't core to Moodle? If so, remove those blocks/mods (resources) from the work copy of the 1.9 course before making the no user backup of the work copy.
Bottom line ... 'scrub' the copy of the 1.9 course before making a no user backup and TIA (try it again).
One could also clean up the course ID folder of the copy in the 1.9 - erase any 1.9 backups contained there in. Then copy that course ID folder to the 2 instance repository directory. When/if, working with that course, and a file link not working or missing, setup a file system repo that points to that course ID folder in the 2 repository directory.
If on a Linux server and both instances of Moodle reside on the same server, one could use symlinks (temporary) from the 2's repository directory to specific 1.9 course ID folders in the 1.9 data folder.
'spirit of sharing', Ken