Joe, VERY interesting article! Thanks!
One of the key observations that I got from this last paper is that, for a given average current (ie, pulse current x duty cycle), you're able to draw MORE capacity from the coin cell with the higher pulse current (lower duty cycle). This is very good news from an operating perspective. The problem, as you say, is how to correlate this to your OTA programming model. Clearly the battery can handle the high current for SOME duration as long as you have a sufficiently long recovery time.
As you've pointed out, how long the battery can sustain the high current can be first order observed by measuring the VBat after each high current pulse (AKA downloaded packet) and deciding how close to the cutoff voltage you dare go before resting. Since presumably you need a response to stop the flow, you need enough remaining voltage to make that transmission (unless you need a response to send the next block - but I suspect that uses more current in burst download mode).
The next important metric would be how long does it take to recover enough to do another burst. This might be the tricky part as you would need to wake up and do a VBat sample to see how much it has recovered. The good news is that you'll never 'accidentally' measure the no load voltage - by virtue of the fact that you'll draw a few mA just to take the reading, so this should show you how much the battery has recovered and, with some amount of experimentation, allow you to project how long before you can check again... a simple heuristic should be able to converge on an adequate recovery time with just a few samples.
Unfortunately, it doesn't take long for the battery voltage to sink down to the low 2.xxx volts so it would be interesting to see if you could do more than 4 1024 byte blocks without resting. However, I wouldn't think you'd need to go to any extremes WRT resting. As long as you can recover enough to get the next 4K block to the device, once it's fully loaded, the device will be able to rest and recover most of its lost voltage, apparently without losing very much capacity.
Even if OTA did adversely affect your overall battery life, being able to do four OTA updates, for example, and still get several months of life it would be a great solution.
Tom