Yes. While I trust the process and have great success with these handsets, it's not something I can recommend without caution.
I need to upgrade from Asterisk 11.21.2 to 11.22 shortly and plan to do this by using the update process in FreePBX first anyway. This will upgrade the system and remove the patch, then I'll just repatch Asterisk and reboot.
The Cisco SIP handsets do work (mostly) without patching, but when you want more, like working BLF, or dual registrations, then the patch is required.
If your FreePBX is running in a VM, then take a snapshot before you start and there is nothing to worry about should something go wrong.