Image Crop Feature
This is a bug with regards to Image crop feature in Illustrator.
While I try to unembed a cropped image (in Illustrator) and link to a PSD source file, the source PSD file gets flattened or layers get merged to a single layer. The source PSD file gets altered and damaging it.
Wait... when you unembed an embedded image, you should not provide an existing original image for this! It will get overwritten with the raster image you have selected in Ai! This is what this command is designed for.
If you want to replace an embedded image with a layered PSD (or any other original source), you should use a different command altogether!
You can use File > Place for that (with the Replace option checked in the Place dialog), or Relink command in the Links panel’s menu.
Why doesn't Ai provide Relink command in the Control menu (or in the context one) — is another question, and I think we can treat this report a s a request to add it there.
Please comment back on if it works for you at all.