I know this is an old thread, but is the first thing that pops up in Google when you search for the same problem, and it was never answered here. I found a solution and wanted to share it. I had the same problem, that when I used %Output Mosaic Layer%\Footprint the model would not run. It said the copy input feature did not exist. However when I removed the percent signs and typed just Output Mosaic Layer\Footprint it did work. Alternatively, I could just select the layer from the dropdown menu. EDIT: Actually this only worked in the Model Builder if I manually ran the Make Layer tool first. Otherwise it continues to fail. helyxsisltd's solution using Calculate worked though.
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