You can search other known folders (with multiMAN, Blackbox FTP, Comgenie, etc) to see if your backups are there. If it is, then point OM to the relevant folders. (I think it gives you an option to select the folder where your games are). If your backups are not there, then unfortunately you have lost them and must copy from your external HDD.
You can use OM to copy the games from the external HDD - it should automatically join the slpit files. If it doesnt, use multiMAN or GAIA to move it back from ext HDD. I know they join the files.