This year at worlds, I used vexnet. The announcers and staff and, well everyone else, STRONGLY encouraged the use of a backup battery. I even think you wouldn’t pass inspection if didn’t have one. Anyways, our robot was having communicating/motor problems. We ended up fixing the communication by retethering our robot to our joystick and disconecting the backup battery, and I was putting too much stress on the motor so we switched it from high speed to normal. However, whenever we went to shut down our cortex, the lights, I believe it was the robot light was flashing red slowly. Was that normal? when we disconected and retethered, that never happened again. Was the miscommunication due to the backup battery?
If you turn off the cortex with the backup battery in, it will flash red slowly, as you described. This is normal, and reminds you to unplug the backup battery.
As far as i know, the backup battery helps keep vexnet alive if you draw too much current through the cortex, so the cortex won’t reset itself (and your autonomous, etc). However, if the backup battery isn’t close to fully charged, it won’t do anything as far as i know, it is only a 9v afterall, and the cortex needs more than that if you draw too much current.
That’s what i think, but i’m sure there is someone more knowledgeable than me out there 
in my local ompetition experiences, teams are better off without a dead backup battery
if the 9v is lower than ~8v, then the robot wouldn’t even function (strange vexnet lights and will not give you control of the robot)
i personally never use the backup batt and nothing bad ever happens because of it
we have heard the same thing. we use the backup (otherwise we seem to have more issues with it dropping), but we change the backup after about every 6 - 8 matches, sometimes even more (at worlds).
I think you guys are right. because looking back now, I realized when I changed the 9v my robot worked good for 1 match, then after that we took it too the practice fields for a while, then it stopped communicating. Thank you guys!
I would only use the 9v for competition games really
we only use it for competition and for programming when it likes to lose connection on us (usually not then even)