Smart objects not updating (CS5)

I am using CS5 Photoshop and when I try to save edits on an opened smart object (eg. after editing a ‘placed’ photograph) a ‘Save As’ dialog box appears. When I save the edits to the smart object, using the prompted file name, they are not reflected in the master document.
Can anyone advise what the problem might be? Is the file path between the master document and smart object being lost?
Thanks for the help.
Justin

Yes I am apply layers to a JPEG. So it's solved by flattening the image and saving, but this mean I lose my fiter and masking layers.
Does that mean the quickest way would be to open the JPEG image before placing, save it as a PSD and then place it?

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