2016 Gen4 clunking rear suspension NOT what you think!

So... reacting to the Tech Service Bulletin regarding rear shocks needing top nuts tightened or replaced, I purchased two brand new nuts and with a copy of the TSB in hand showed up at my local Toyota dealer asking that the shocks have the service as outlined in the bulletin provided. 1:5 hrs. of service later and $200 poorer I was dismayed to feel the ride was tighter but the noise, the clunking over bumps, was worse. I took it to another garage where two techs spent 20 minutes analyzing the problem and then gave a diagnosis: Bad shock drivers side. Two of the worlds most expensive shock absorbers were airlifted to the garage and the next day surgery was scheduled for 2pm (1400hrs). At 4pm their top mechanic said I put your original shock back on as there was nothing wrong with it, and I found the problem. The rear brake calliper bolts had loosened and one bolt had fallen completely out, I replaced both bolts and noise is gone.
Needless to say I was shocked!

 

52,000 miles so past the warranty for the nut tightening work.

 

yes I do use the e-brake. And I had the emergency brake recall work performed for free. Is the emerg brake only on the rear drivers side? could the dealer have screwed it up while performing that task??