Obfuscation by definition changes the names of functions, and if you try to call a function by its original name from a non-encoded context it's going to fail. Examples would be calling a function in an encoded file from a non-encoded file, or a function name passed to array_walk(), or any other non-encoded function that makes callbacks.

Create an obfuscation exclusion list (empty text file), add the original name of the function that is not being found, and tell the Encoder not to optimise functions in the list. To help identify the function, turn off line number obfuscation for now.