When you pause protection of a Hot Folder, only the files already protected by that Hot Folder before pausing protection will continue to be protected - regardless of where they are sent. However, new files placed in the Hot Folder will not get protected until protection in the Hot Folder is resumed.
Pausing protection on a Hot Folder is similar to deactivating it temporarily. The Hot Folder can be activated again at any time - and will continue to function as normal.
To pause protection in a Hot Folder, follow the steps mentioned in Editing a Hot Folder to log in to a Hot Folder Cabinet and selecting a Hot Folder. Scroll down in the right panel and click Pause.
You will be prompted to stop the Hot Folder Service. Once the changes are saved, restart the Hot Folder service to resume monitoring of Hot Folders.