I had the same issue, but I seem to have gotten both accounts into Codex now. First I logged out of GitHub from either account. Then I go to environments (top right), then Data Controls on the left in Codex. I disconnect from the first GitHub account that I was connected with and then connect with the 2nd account (It will say it is connected to the 2nd account).
Then go back to environments and add any new project(s) from the new GitHub account. Now you should see projects from both accounts in the environments table.
I then asked it to summarize a project from account 1 and separately from account 2 and it seemed to work.