So, I need to manually remove the 'backup' folder before 2nd "apply"?
Viewing post in Chastity Belt Mod v1.2.2 (for Strive v0.5.25)
No, you need your backup folder to not be deleted before the 2nd "apply". Your problem is consistent with it being deleted before the 2nd "apply", though there could be another cause. If there are no other mods or alterations to the files, then the most likely sources of the problem are user error, or file system interference.