Am a little confused as to goal here, but as to the finding of the 1.9 backups (if they exist in the 1.9) ... every course has a ID number which is found in the moodledata folder. Course ID #1 is the folder for the front page in a 1.9 version. The other # folders are the individual courses and in each there is a backupdata folder containing the backup files. Those #'d folders may not be sequential - ie, 1,2,3,4. Gaps means a course that used to exist has been deleted thus no course ID folder.
Sounds like you are planning then to upgrade the 1.9 site to a version 2 ... which is a major undertaking. What I've found ... if the backup zips remain in the 1.9 when migrating the site, their presence just makes the migration process work harder - ie, the 1.9 backups are just taking up space and requires heavier processing during the migration process to move all the backup zips into the new Moodle 2 file system. As a prelim to migrating a site, I usually archive the 1.9 backups to some other location ... one can still use them for course restores in a 2 later, although they each might issues of their own when restoring to a 2.
If the goal is to get Moodle 2 backups made from the 1.9 courses one might find installing a fresh 2 and then working with importing the 1.9 courses to get them in a 2 format an 'easier' path.
Others ... might think differently.
'spirit of sharing', Ken