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That shouldn't be the case. The option you've mentioned is in the conversion settings and thus only applies (or should only apply) to conversions. The only way I know of to change metadata when sending to the device is via plugboards.
It may be that you've set it and sent a file to your device with no suitable format for your device, in which case Calibre should start to convert the file, thus applying the setting you've mentioned. That would certainly create the impression that the setting applied to sending books to devices.
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