[kamocat]

A heartbeat or trusted command is required every 100ms for a Jaguar to stay enabled.
(The "set output" messages are trusted commands. The heartbeat will keep all the Jaguars enabled, but if you want to use trusted commands, you will need to update the output of every Jaguar that you want to keep enabled.)
I believe resuming the heartbeat will NOT cause your motors to move again if the output is not re-sent. (This makes sense with the behavior I remember, but I have not explicitly tested for this behavior.)

EDIT:
mjcoss, I can probably answer some of your questions.

Yes, in updating all your motors every 10ms, you will see many timeout issues. Setting the output takes 5-10ms (often 8ms) for a single Jaguar.

Autonomous is likely more sensitive than Teleop because Teleop sends the output continuously(Theoretically this is every 20ms, but with 4 Jaguars it could be as slow as every 40ms. In LabVIEW, the drive motors are dealt with in near-parallel, which reduces the time by about 50%. I don't know if the other languages do this as well.)
In Autonomous, the output is usually only updated when it changes. This means that if the heartbeat is temporarily prevented from getting through, it will not do anything when it finally DOES get through, unless you've used a trusted output command.