Actually you started out with the Asterisk for BBB image (
http://www.beaglebone-asterisk.org ) also known as RASPBX for BBB which has Ubuntu, Asterisk, FreePBX, Hylafax, chan_dongle and Exim 4 precomplied and pre-loaded. It's a turn-key FPBX system that you simply load on a Micro SD card and boot your system. That is not a product of PBIAF. The Incredible PBX script for BBB is a product of PBIAF. When you run the IPBX script on top of your running BBB-RASPBX system, it does not significantly alter anything but does modify some of the existing programs and settings and also adds programs / settings that are required to run the IPBX features. IIRC, it does wipe your existing Asterisk/FPBX settings. Best bet is get your BBB running and updated with the base RASPBX image (but don't set up any trunks or any other permanent PBX settings), resize your SD card, run the IPBX scripts, reboot into RASPBX with IPBX , make a copy of the system disk with the 'raspbx-backup' utility (keep the copy in a safe place in case you goof up your system later) update that resultant system and then run a FreePBX backup of your base RASPBX-IPBX base system (keep copy offline for later restore if needed). Then add your trunks, extensions, whatever. Then backup with Freepbx again and store the B/U offline. If you have some additional storage space on an flash drive, do another raspbx-backup of your fully configured system and store that offline as well. That way if your SD card craps out you only need to restore the raspbx-backup created image and then restore your latest FPBX backup on top of that.
This guidance is provided having used this system for the last year or so.
Also, if your BBB ever hangs during an 'apt-get update && apt-get upgrade -y', you may want to try the guidance provided at the bottom of this webpage:
http://askubuntu.com/questions/4694...-error-ubuntu-14-04-unable-to-install-updates . My BBB would hang setting up the updated udev or mysql or whatever. I didn't discover this work around until recently having spent countless wasted hours of frustration trying to update my BBB RASPBX system. In fact I got so frustrated (o.k. I was pissed) I put it away for awhile.