The most straight forward way would be to schedule your RemoveExistingProducts after InstallExecute or InstallFinalize. That way the config file is not removed and then installed again (like if you schedule before InstallInitialize). Of course, scheduling RemoveExistingProduct so late means you need to be very careful about your Component Rules.
If not in cases like this I assign the config files to their own components and mark them as Never Overwrite. This way upgrades will not overwrite the file but uninstalls will remove it.
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