I was able to perform the firmware flash for both radios: "API coordinator (1941)" and "API End Device (2941)", but when I attempted to read the End Device using X-CTU, I got the following error:
"Failed to enter command mode
Unable to read Version (ATVR)
Read parameters.. Failed."
After a few more attempts, the read succeeded but when I clicked "write" to save my configuration I got a similar error:
"Getting modem type....OK
Programming modem...Lost communication with modem
Write Parameters...Failed"
Woe ensues. As it turns out, the default sleep option for "API End Device (2941)" firmware is SM=4 (Cyclic Sleep); the errors occur because the radio is periodically going to sleep and waking up. Unfortunately SM=0 (No Sleep) isn't even supported in this firmware, but there is a solution. To simulate No Sleep, configure the radio to SM=1 (Pin Hibernate), and then connect Pin Sleep (pin 9) to Ground (pin 10). Credit goes to Hans (XBee-API user) for this idea.
Now to program the radio we still have to fix the sleep issue. To do this we can use the Reset pin (pin 5). The Reset is activated by connecting the Reset pin to Ground (pin 10), and then disconnecting. If you have a toggle switch handy you'll want to wire this to pin 5 and pin 10. (Remember if you are using, XBee Explorer USB, there are two extra pins (GND and 5V), as shown in the diagram)
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Now toggle the switch on/off just before performing the X-CTU action (e.g. read/write). Once you have configured the radio to Pin Hibernate mode and grounded pin 9, the radio won't go to sleep and you won't need to use the Reset pin anymore.