For anyone still struggling with this, I have a solution.
Longtime fan of FoG2, I've recently sold my gaming PC and moved over to the Steam Deck. For anyone else wanting to have Windows-like cross-compatability between FoG2 and Empires, the easy solution in Linux is using symbolic links within each prefix. These soft symbolic links will let the games communicate, and they update automatically too.
Here's the step by step process, for all eight of us who play these games on Deck:
1. Navigate to your 'My Games' folder within the FoG Empires prefix (e.g., '/home/deck/.steam/steam/steamapps/compatdata/YOURPREFIXNUMBERHERE/pfx/drive_c/users/steamuser/My Documents/My Games/'). Confirm that the folder 'FieldOfGloryEmpires' is within this 'My Games' folder.
2. In a new window, navigate to the 'My Games' folder in the FoG 2 prefix and open the 'FieldOfGlory2' directory within. Copy the whole path to the clipboard.
3. Open the terminal (Konsole) within the /My Games/ folder in FoG EMPIRES! (you can do this simply by right clicking within the folder, and choosing 'open in Konsole' from the drop-down menu).
4. Input the command below, and paste the full path for the FoG2 folder so it looks like this (only with the correct prefix number for your Steam Deck):
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ln -s '/home/deck/.steam/steam/steamapps/compatdata/FoG2PREFIXNUMBER/pfx/drive_c/users/steamuser/My Documents/My Games/FieldOfGlory2/'
Don't forget to change this to your actual prefix path, and put quotes around it!
5. Now, close that Konsole window and copy the full path for your 'FieldOfGloryEmpires' folder within the Empires prefix 'My Games' folder.
6. Navigate to the 'My Games' folder within the FoG 2 prefix, and open up the Konsole there.
7. Input this command to do the same for FoG 2, now, as we did for FoG Empires:
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ln -s '/home/deck/.steam/steam/steamapps/compatdata/FoGEmpiresPREFIXNUMBER/pfx/drive_c/users/steamuser/My Documents/My Games/FieldOfGloryEmpires/'
Once again, don't forget to make sure the command is using your actual prefix path (not my example path) and that it's enclosed within 'single quotes'.
8. All done! Now the process is just like Windows - the contents of these folders are visible to each game and you can export directly to FoG2 from Empires without copying any files.
To confirm that everything has worked, when you open up your 'My Games' folder within either of the games' prefixes. You should see two folders, one for each game. One will be in italic font (that's the one that was symlinked into the folder). I've attached a screencap of my FoG Empires prefix 'My Games' folder as an example.
If you're having trouble finding your prefix folders for each game (the specific numbered folders within '/home/deck/.steam/steam/steamapps/compatdata/'), just load each game up and make a new save in each. Then you can sort the folders within /compatdata/ by 'Last modified', and the top of the list will be the folders for FoG 2 and Empires.