Hi Leanne,
While loosing referral traffic due to the changes is less than ideal, I would lean towards moving on in this instance.There is nothing in your listing that specifies a customer cannot customize your template files as they wish after purchase.
I see in your shop policies you say "It is illegal to distribute, copy or manipulate our products in any way, shape or form without permission" but if this includes changing any part of a template I think it could be clearer as most template files I have encountered are not sold in this way.
Do you sell your templates at the specified price because your business model includes the benefit of referrals from existing installations or do you think your pricing is fair value for the design and code you offer. Either way it may be an opportunity to evaluate your listing details, shop policies, or maybe even your post purchase expectations to add clarity to match.
Great shop by the way! Your designs are awesome.