Cause all the .php files containing lines ending with \r\n to instead end with \n.
DYI with:
find fusionpbx -type f -name '*.php' -exec dos2unix '{}' \;
Users: Adjust so assigned Domain doesn't get overwritten if user_all permission exists, but user_domain doesn't.
Destinations: Adjust so assigned Domain doesn't get overwritten if destination_all permission exists, but destination_domain doesn't.