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TTN Mapper will use the location configured on the TTN Console first. If the location is not configured there it will use the location which the gateway reports. That means that a gateway with a built in GPS will be located at the location set on the Console, not the location the gateway reports. Only if the location is not set on the Console the fallback location - the location reported by the gateway - will be used.
https://ttnmapper.org/faq/
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