No, The ESP32S3 does indeed have 2 com ports but you have to put the Core S3 into Boot mode to program it.
In most cases it's the USB cable or the Host PC that is the problem. Windows has issues with its come port communications with S3's. huh, what, All firmware is available in M5Burner unless you made it yourself then you should be backing up your own files. Never heard of CoreS3 TP Upgrade V0.5.exeM5Burner is the program for burning firmware.