Save them as a "flat" format like TIFF or PSD with all your adjustments baked in.
Then can I convert them to JPEG as a batch savving the changes?
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You can save them as jpegs from ACR using ACR's Save Image(s) button. Set the Destination in the ACR save dialog to point to a different folder (from where you have source jpeg files). Jpegs you save using the Save Image button should open in Photoshop; jpegs you've 'saved' via the ACR Done button will open in PS via ACR.
Thanks! I'll give it a try.