Take a look at the logs in the Console App and see if anything is showing up there regarding the disappearing apps. Any crash or unusual exit should be reported there. Console logs don't always work the same way in Sierra as in previous OS X versions and it may take some hunting to find the entries and they can be difficult for anyone but a developer to fully understand, but they can be helpful in a case like yours.
If you find something and need help post 10 or 12 lines either side of the entry back here and someone should be able to help figure it out.
