Atomic information is stored in session files as compressed Python data structures, not in PDB format, so there is no practical way to make the swap you are envisioning by editing a session file.  Nonetheless, using Python you could copy coordinates from the model you adjusted in Coot (assuming the adjustments didn't add/delete atoms) to the model restored from the session.  I've attached a script (copycrds.py) that if you open it ChimeraX will define a command named "copycrds" that allows you to copy coordinates from one conformer to another (e.g. copycrds #1 to #2).  The script and description is also on the ChimeraX Recipes page.