Go to C:\ProgramData\Microsoft\Windows\Start Menu\Programs
. Make sure the programs that are on your second drive are in here. If your shortcuts inside the folders listed there do not have an image, it seems to be a problem with ownership.
Go to C:\ProgramData\Microsoft\Windows
and right click "Start Menu" -> Properties -> Security tab -> Advanced.
At the "Owner:" field click Change and type in Everyone and click "Check Names". Everyone should be listed there and click "Ok". Check "Replace owner on subcontainers and objects". Now click on "Everyone" in the list of "Permission entries:" and click on "Edit" and give full permissions.
After that make sure you check "Replace all child object permission entries with inheritable permission entries from this object" and click "Apply". Your shortcut icons inside the Programs folder will return and Windows can find all your applications again. I do not know what broke this in the first place. This is how I fixed it on my end.