Disappearing (non system) icons in dock

every now and then non-mac icon will disappear and get replaced by a ?

The ? indicates that it can't find the original application. If you install any app, you should install it in the Applications folder. Once installed there, drag the icon to the dock which creates an alias/one click access to the app.
So, check where the missing app is located. Then simply drag the ? out of the dock and replace it with the real app icon.

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