Photo becomes gray after merging or saving it

You have at least one Layer Mode set to Lighten.  In my experience flattening documents with layer modes set to other than Normal, can sometimes lead to weird things happening.  This seems to be even more likely when Smart Objects are involved.  My workaround is to select the topmost layer, and add a Copy Merged layer to the top of the stack (Shift Ctrl Alt E) before merging or flattening.  As far as I can remember, this has never failed to fix this sort of situation.

It was actually only a few days ago the last time I ran into this, and from an interest point of view, I spent some time trying to isolate why it was happening.  And failed.   I'd have liked the satisfaction of having worked out — it would be like solving a puzzle — but I tend to take a black box approach to stuff like this.