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The Default location for Pass the work folder as the first argument:
is ...\JEPlus\jEPlus_v1.5.1\output\
.
I think you should not do any thing with it as long as you are not using python. What you should do is change the result folder of ReadVarsESO to the one where you want to save your results. JEplus will save your results in that folder OR you can leave it as default and jEPlus will save the results in the default folder, which is the same as I mentioned above.
I hope this will help.
May be @Ivan Korolija can throw some light on this.