Manually editing ProgramApps.ini (in ProgramData\Reshade\) in order to remove an app doesn't make a difference. Is there another file that decides which apps to hook into?
ReShadeApps.ini is only used by the setup tool to keep track of how many apps it installed to (so it can completly remove ProgramData\ReShade once it was removed from all apps).
ReShade itself checks if a ReShade.ini file exists in the app directory and only loads if that is the case. So as long as the Vulkan layer was registered, you can enable ReShade in any Vulkan app by creating a ReShade.ini file next to the executable and disable it again by removing that file.