no, they can be anywhere. xbla games that is. I think dlc has to remain in the content folder. you don't need to hold down a button to play a different region game. yaris swap just replaces the header of the content. have you examined the content with yaris swap? maybe try patching again with that app instead of something else.
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wait a minute. this just hit me. I think I know what is causing your issue. the database of FSD/Aurora contains a copy of the serial number for the hdds being used, so it's probably not matching up with the new hdd. delete the database (in settings), and rescan.
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wait a minute. this just hit me. I think I know what is causing your issue. the database of FSD/Aurora contains a copy of the serial number for the hdds being used, so it's probably not matching up with the new hdd. delete the database (in settings), and rescan.