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No, saving as a JPG does not damage the pixels as such. You do your work in Camera Raw with the Raw file, then Open in Photoshop and do your edit, it can be any format you want it to be when saved from Photoshop. If you know you are going online with it use the Save for Web under File. I would save as a PNG which is a good format and is not "lossy" as JPGs are sometimes described.

There is also an option in ACR to save as a Smart Object in PS and the ACR edit will be available from PS. Suggest you do some reading on the use of ACR particularly since you are a photographer.