In the 2 instance, one has to turn on File System repos first.
That should create a 'repository' directory in the data folder for the 2.
Make notes on what course is what ID number in the 1.9 version. You'll need that info to link to the correct repo later.
Then copy the course ID numbers from the 1.9 data folder to the moodle 2 repository directory. How one does that depends upon what access one has to the server.
Do you have command line (shell) access? Have some other tool that will allow browsing of files in the data directories?
I can describe the command line, but don't remotely host on shared systems so don't use any of those kinda tools.
From this, however, one should get an idea:
moodledata19 contains the course ID folders: 1,2,4,5,10,101, etc.
you have a moodledata2 at the same level of the file system/structure:
cd /var/www/moodledata19
cp -rp ? /var/www/moodledata2/repository/
the -rp is recursive and keeps permissions on folders files.
the ? gets all single digit folders.
Repeat command to get double digit folders:
cp -rp ?? /var/www/moodledata2/repository/
and same for any triple digit folders:
cp -rp ??? /var/www/moodledata2/repository/
check to see they are there:
cd /var/www/moodledata2/repository/
ls -l (list long to see permissions)
After you've got them copied, log into the 2. And then to a course where files are missing. In the Course Admin menu, go to repositories and establish a file system repo for that course (remember those notes it was suggested you make concerning what course ID number was what course?). Name the repo anything you like but the numbered folders you copied over should show in the pick list of available file system repos - which are really the course ID folders you copied.
That help?
'spirit of sharing', Ken