We've been doing maintenance on the Japanese cars since 2001, mostly Subarus, and probably have had a dozen or so that needed warranty work, our documentation has been accepted in each and every circumstance where it was needed to get a replacement motor or other warranty work. There should be no issues if you go to a reputable aftermarket shop as long as they document it all for you.
-mike
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 '14 Touareg TDi | '04 Nissan Armada | '13 Subaru BRZ
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