Hi AJ,
This is an unusual setup so I am only making suggestions and observations.
Usually if doing a formware upgrade, the other capabilities in the system are disabled.
If however your application requires continue collection of samples at the 15ms rate, you would have to buffer the sample to RAM until the firmware update is complete and then copy the buffer to your desired location after the firmware upgrade completes. This way you have minimal delay during firmware upgrade.
I usually see firmware upgrade as part of a bootloader application so that if there is a brown out (power failure) during upgrade the system will recover and restart the bootloader application. I have not seen a bootloader collecting data samples too.
Best Regards,
David