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It wouldn't surprise me if they had a system setup so they charge people the sometimes extortionate full retail of an individual boxed cable kit then just fit bulk out of boxes. As a result the new guy hasn't got into understanding how to explain the system in a way so that the customer doesn't know about the bulk box of cables in the workshop.
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The Edinburgh Bike Co-Op would have sorted you out; I can't talk for Evans' workshop stock policies but dicking you around for an inner that most workshops will carry in bulk seems a bit rich. That said, perhaps he was just trying to upsell you as new inner + new outer (which you already had) = better performance. Either way, there's a right way to keep the customer happy, and it's not like you were after a totally obscure part.
A letter I have just written to evans customer service, bloody jobsworth!
TLDR - Needed gear cable inner, evans only had it in the workshop, jobsworth manager wouldn't sell it to me, flounce!