Photoshop CS4 smart object template just overwrote a raw file - HELP

Question

So.  I've been working in Photoshop extensively for about 6 years now and I am well aware that nothing we do in Photoshop or Lightroom is supposed to overwrite a raw file.  I'm not talking about changing it to something a little lighter or darker, I'm talking about replacing a picture of one baseball player with another one - and the original? Gone. 
Here's what happened: I have a poster template that contains several layers, 7 of which are smart objects.  I change the pictures in the template by right-clicking the smart object layer and selecting "replace smart object," browsing to the new image, selecting, and here is what SHOULD happen: the target picture opens in Adobe camera raw, I make some small edits, click done or okay or something similar, and that new image has replaced the old one in the template.  What DID happen was this: I followed the procedure above and selected my target raw file, the picture that was already in the template (the one I was trying to replace with my target file) opened in Adobe camera raw.  I thought - Hey, that's wierd!  Closed the ACR dialog and tried again.  Same thing happened.  I opened lightroom and saw - to my HORROR - that the target file had been changed to the same image that was in the template.
If it clarifies: pictures of player A (who played in 2009) is in all of the smart object layers in my template.  I want to make that poster be of player B (who played in 2012) so I begin replacing all the smart objects.  When I get to the 3rd image in the poster template, Photoshop overwrites my raw file of player B with the smart object photo of Player A.  There were no photos of player A on the network drive that the picture of Player B was on.  But there's one now.  My raw file shows that it was modified about 10 minutes ago. 
We tried undoing in Photoshop.  That did nothing.  We tried deleting the xmp file.  That did nothing.  We removed it from the lightroom catalog and reimported it.  It is now a picture of Player A from 2009 and my picture of Player B from 2012 is just gone. 
Anybody have any idea what this could be and how we could avoid it in the future?
Best,
Jamey

Answer 1

mojoimagery wrote:
Now - JJ - when you say "overlay files" - what do you mean?  Because that feels like a good description for what happened.
We performed no save operation at any point during the sequence of events that ended with the image in one raw file being replaced by the image in the smart object.
As I wrote Smart Object layers embedded object is a copy of the original  and if you replace it you replace it with a copy of some other object. Embedded object are copies and independent from the original.  If after creating a smart Object layer who's embedded object is a copy of a raw file and its conversion settings. You change the original RAW files RAW conversion settings the smart object layer raw conversion setting are not changes for its a copy with independent raw conversion settings. When you replace a smart object layers contents you will replace the embedded object and you should replace it with an object the has the same pixel size and orientation. Because there is an associated transform for the object in the layer that is not replaced. The replacement is also a copy.  If the original smart object was created using  File Open where you choose a RAW file  ACR would open with the RAW files current conversion settings.  In ACR you can changes the setting then hold down the shift key to change the open image button to an Open Object button.  Using that button ACR will open a smart object layer in Photoshop the contents of the embedded object is a copy of the RAW file and the current ACR settings.  No File is written Photoshop is not a File Editor its a Document editor that has many data structures for different layer types.  When you replace the contents of a smart object you will be put into a "Place" file selection dialog if you choose a raw file it should have the same orientation as the image being replaced because of the associated transform. When you choose a RAW file ACR will open and you can change the conversion settings however there will be no Open Image button instead there will be an OK button.  There is also a save image button and you can save a RAW file that is a DNG file not a CR2 file. Like the DNG converter. If you click the OK button the embedded object in the smart object layer will be replaced with a copy of the selected RAW file and the current ACR settings. Again there is no file written Photoshop is not a File editor just the embedded smart object data is replaced in Photoshop smart object layer's data structure.
I do not think the use of smart objects in you process caused what you are experiencing and because it only happens once an a while I feel its more likely caused by some human error made during the processing in those cases. I would look elsewhere for what causing the overlay. In the place file selection dialog it is possible to rename files perhaps even by accident. Programs like LR and Bridge can rename and copy files perhaps overlay other files.