Container/Portainer apps not getting deployed properly all of a sudden.

That’s just the containers filesystem. Like you need to find the correct path, but CS isn’t setting up a truecrypt image and hiding all of your stuff.
Your SimpleHelp containers filesystem contents are just raw sitting on (by the sounds of it) container-station/docker/volumes/.
Attach to the container, ls -l /, look for that file structure in the CS qpkg install directory.