If you use the "Hide in this flow map" but want to later recover the hidden item: Click "Application Flow Map" at the top left of the flow map, in the drop down select "Edit Current Flow Map". Look through the options. In my case it was the Databases & Remote services that has a visibility and grouping section. One of the columns is Hidden, and I was able to find the object I was looking for and uncheck the Hidden option. The item (a queue) was restored to the flow map.
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