How can I update a map/mesh and coordinates in a PyMol session file?
Until someone identifies an ‘update’ function in PyMol, I think the next best thing is to use scripting. (See the pymol wiki) It is an imperfect solution, but it may work for the situation presented in the original post if the session may be reproduced.
To begin capturing the commands in PyMol, including menu selections to a script file, select:
File -&gt; Log File -&gt; Open -&gt; myscript.pml

When done with creating the display panels, select:
File -&gt; Log File -&gt; Close

The input data files and the script itself may then be updated or replaced. In a fresh PyMol session, execute the script with:
File -&gt; Run Script -&gt; myscript.pml

To test the above, I generated a PyMol session where I captured a script as above. I loaded the atomic coordinates of a small protein, a ligand and a 2mFobs-DFcalc electron density map. Then I displayed some panels along with mesh surface around the compound. The co-structure was then re-refined, thus generating modified atomic coordinates and electron density maps. I replaced the original files with the updates and executed the script in a fresh PyMol session. The display panels were updated accordingly.
I recommend the Advanced Scripting Workshop.