tbh... your locksmith analogy isn't correct... it's more aligned with software, you pay for Windows 7, Microsoft doesn't give you free access to mess with the code to make changes and render their product unusable. anyway...
i'm newer to all this than even you, but is it possible when they've taken it off the dyno something wasn't reconnected/tightened/untightened? if you consider the symptom of spluttering over 6,000kms (and disregarding the tune) what might cause this? coils? boost leak?
Just a late night snack...