This happens when you move your animated layers from one location to another. After effects looses the location and therefore can no longer read the layers you have been animating. If you right click on the layers and select replace footage....you can then relink the layer to the correct location. Once relinked After Effects should automatically relink other layers in the same location. If you have layers in multiple locations you might have to do this more than once.
You're a legend! Thanks! I thought it might have been something like that as I had reorganised my files.
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