EQ2MAP will only attempt to overwrite the eq2.ini file if you have EQ2MAP installed outside of your custom UI folder and run the EQ2MAP Patcher. To avoid this just make sure that EQ2MAP is installed inside of any custom UI folder that you have created.
FYI: setting the eq2.ini file to read only doesn't help since the EQ2 Patcher will see the read only tag and assume that the file needs to be replaced with the default. This is what is more than likely causing your problem.
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