There are legal/contract issues here that I'll leave for others.
Mechanically, it is your mechanic's decision to reassemble or not. Let him decide.
Once he has done that, it is also his decision to refit it (or not).
Always a chance they did find the cause but were too embarrassed to say so -or disclose what damage)if any) was done.
If it is installed and makes the same noise see Post 3 above.
One of the many difficult stages of working on the 6 speed is refitting the case over the internals. Simply put, the shafts are often reluctant to go in the correct holes. That may have been the cause of the noise ?
An experienced rebuilder of this gearbox(also used by Audi) would have a good idea what the issue was.
https://jhmotorsports.com/shop/catalog/01e-speed-full-rebuild-kit-jhm-performance-jhm-updated-collar-p-2054.html
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