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Are you talking about saving from Camera Raw?
The changes made to raw images can only be saved in Camera Raw. Those changes are not stored in the raw image, but rather in an XMP sidecar file. Once the image has been passed to Photoshop and has been edited in Photoshop, it has to be saved in a different file format. The raw images are read-only. Neither Photoshop nor ACR make any changes directly to the raw image itself. So if you have started working on an image in Photoshop, and want to do additional work later, the best thing to do is save your work as a PSD or tiff image. Either one of those formats will preserve all of your Photoshop changes, including adjustment layers.
As far as making changes to the raw image is concerned, when you click on the Done button in ACR your raw image changes have been written to the XMP file, and that file will be read by ACR when you open the file again.