Sent out for simple repair, came back unbootable.

• Brought my mid 2015 macbook pro with applecare to my local store due to a thunderbolt port issue. (Port was simply broken and not recognizing any device.)
• They sent it to the main repair facility, and replaced the entire logic board. I got it back within 5 days of bringing it in.
• Got home, went to boot up the computer... and couldn’t. I did all of the troubleshooting I could (various resets) and attempted automatically repairing drive in disk utility, but couldn’t as it wouldn’t load past “select a drive.”
• Walked back into apple store 2 hours later and they took me right away (of course). Technician proceeded to try the same resets… ultimately, they all didn’t solve the issue. He recommended "wiping and using the backup external." We wipe the computer, and he says "you can try and recover it here, or you can go back home to do it cause it may take some time." Decide to go home as I have 500gb I need to restore.
• I restore the drive (took 5 hours). Go to boot up.... won’t boot. 

What gives? Should I complain about a faulty machine? Should I complain about apple returning my MacBook in worse condition than it was before? Very distraught as I’m self-employed and rely on this machine for work... not to mention, I’ve thrown buckets at this company having purchased 3 iPhones and 2 other MacBooks. I should not be dealing with this failure within 3 years of purchase. (I purchased the computer in early 2016 brand new as I was told by a rep that the 2016 Touch Bar models were getting recalled/complaints.)

Also, if there is a ‘’bad file’’ in the backup... am I just expected to manually drag files over from time machine and redesign my system?

I work with audio- it will take me hours to redesign my machine and audio plugins as well as application support folder... not to mention, redownload all my programs. I really don’t feel I should be expected to do this.

Any advice would be great.

Thanks!