I guess you already tried what is detailed in the first post:

* If you uninstall this app it will leave the Backup files in MyDocs (/home/user/MyDocs/.N9QTweakBackup) and if for some reason you forgotten to restore your tweaks before uninstalling or just want to restore later, you can do this manually or only one time by running the one simple command as ROOT: sh /home/user/MyDocs/.N9QTweakBackup/RESTORE. This command:

restore your tweaks to default (except the new IM’s)
Delete this folder (.N9QTweakBackup) from your phone
Refresh your home and lockscreens