I am using FreePBX (Distro) 3.211.63-5 with Asterisk 11.3.0 and Digium Phones Config FreePBX module version 22.214.171.124 (From the FreePBX Repo and manually downloaded from Digium doesnt matter). Didnt try AsteriskNOW with FreePBX to see if it wipes the firmware directory there too.
Even before the FreePBX module appeared for DPMA, any time I uploaded either a new module, or downloaded an upgrade module (Both local and from the repo in FreePBX), it wipes out any firmware located in /var/www/html/admin/modules/digium_phones/firmware_package
And displays an error to the effect at the top of the FreePBX web page.
The simple solution is to manually download the missing version and untar/zip it in the same folder to get rid of the error and continue to be able to upgrade firmware on Digium phones from that point on.
Also, until you download/replace the missing version(s), the “check for updates” button does nothing.