I completely agree with the moderators here. When you pointed 8.4 to the Content Store of 8.1, 8.4 would have stamped the Content Store and it is not backward compatible so now your Content Store cannot be used in 8.1 When you installed 8.1 again, did the Configuration even test properly?
If you have a backup of the Content Store BEFORE you pointed 8.4 at it, then restore from the Backup and use that in 8.1
The reason your user's reports did not show up in their My Folders is because something went wrong when you pointed 8.4 to the Content Store of 8.1. It is a safe way to create a new Content Store for 8.4 and use Cognos deployment archive option to dump and load the entire Content Store.