Great question — answering as the UphillTech team:
If you have a host of legacy data with this separation, you are better off leaving it as it is . You can usually sort this out in your reports, so having consistent data is best. In contrast, if this is a new partner, you should keep the medium consistent and use "affiliate". You never know what dimensions or metrics will reveal important data. If you have to set up segments or manage report filters because of this medium inconsistency, it may be troublesome to get to the correct view quickly. Keep in mind that the optional "campaign content" parameter can be used to differentiate the specific content that was clicked.
Full answer by MXMLLN: https://webmasters.stackexchange.com/a/82308 (CC BY-SA 3.0).
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