If what you say is true, they are truely on one circuit, then you should troubleshoot as you mentioned.
I would be very suspicious why it suddenly happened at the same time as replacing the main box. I would guess that the dead circuit is not wired into the box at all or properly.
However, if you can easily trace the wires for this circuit and it is truely one circuit, you problem should be in the last functioning switch or receptacle. Thats why many codes require pigtail leads to the receptacle in the box. In case the receptacle goes bad, downstream items won't be affected.
Merry Troubleshooting, and a Happy New 200 Amp Service. Ho Ho Ho