Simply install the complete UI according to its instructions and then re-run the EQ2MAP updater; if your new UI was installed properly the updater will detect that and load the maps into it.
You can save a little bit of download by copying some files from the old EQ2MAP UI folder into your new UI folder, just don't overwrite anything in the process or you may alter your new UI's look. Or don't and just let the updater redownload it, it shouldn't take all that long.
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