From what I re-call the upgrade process does files first. Sooooo .... what does the moodledata folder now contain? Are there 'digit' folders: 1,2,4,12,15? Those are course ID's in 1.9.x. If they exist, what do they contain? One could see humanly re-cognizable file names ... somepowerpoint.ppt, etc..
If the only thing they contain is a 'moddata' folder ... ie, no document files/image files, etc. afraid the attempt has restructured it all.
Is there a 'filedir' directory? That's where your files now reside but that directory can be used only by version 2 of Moodle.
Not having a backup of the moodledata directory isn't good. At this point, your only option might be to continue to move forward and get the 2.2.9 to work - if possible.
Would strongly suggest getting at least a SQL dump of the DB that you have currently. Make sure you name that dump in a way to indicate that it's a 2.x dump and not a 1.9.
In order to help with that some specific information needed: remotely hosted? If so who is hosting provider? Windows/Linux?
'spirit of sharing', Ken