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[Heimdall]

You almost certainly can't do that. The xbe probably saves its settings in a single, numbered folder in E:\UDATA\, and that is the same folder for both copies of your xbe.

If you use UnleashX as your dash you could write an UnleashX script to copy the contents of the appropriate folder to and from two separate holding folders before launching the copies of the xbe files. You'd have to copy the folder contents back to the relevant holding folder again if you make any config changes, or you'd lose them next time you run the script.

[hcf]

Heimdall is right. In the past I tried to do something similar (the same emulator with different skins in different folders) and I even tried using a different version of the emulator in each folder, with the hope that each version saved its data in a different place... but I didn't have luck, because the reason that Heimdall pointed.

I tried this with Neogenesis, but I guess that mednafenx does the same...

[madmab]

There is a thread around here that explains how to trick the emulator into using different saves directories without running into a conflict.  But I'm not sure where it is.

You could also hex edit the XBE file like most people do.