Bug with Cropping/X/Y movement of initial clip, once you use "Replace with After Effects Composition".
Place a clip in Premiere. Move it (x/y). Scale it.
Add a "Crop Effect". Crop it.
Then, right click, "Replace with After Effects Composition".
Fix something. (Remove Grain Effect). Save
Go back to Premiere.
Problem is: it forgets that it was cropped. However (key point) it DOESNT SHOW YOU that it's no longer cropped. In Premiere it still looks cropped. But Export it, the cropped area is replaced with pure black.
(There were multiple layers, and this was near the bottom).