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I have a project that makes heavy use of the essential properties feature within After Effects (not exporting them to MOGRTs for Premiere).
I have a template set up that is placed several times within a parent comp. There are a variety of properties open to modification in this template including text controls, positioning, visibility and media replacement.
When I duplicate one of these instances, about half of the time it works fine and I can modify the duplicate to be a new instance with no problems. The other half of the time, however, the media replacement options disappear from the list of essential properties for that layer. Every other property is fine, and the layer retains the media used in the original that it was duplicated from. Just the media goes missing.
I can, of course, just drag a new instance in to the scene, which has all of the options open. However, my scene uses some intricate placement of layers that makes duplicating and shifting far easier than having to reposition a brand new layer.
Running AE 18.4.1
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Without understanding the actual structure of your project and timeline, potential involvement of expressions and so on nobody can tell you much. Cropped screenshots are essentially useless. That said, it pretty clearly sounds like you created a cyclic connection somewhere so AE doesn't think it needs to recalculate the internal IDs and/ or ditches references to footage. So for what it's worth, we definitely need much more info and better explanations.
Mylenium