While I don't have a explanation of why you are seeing this error, I have a suggestion to rewrite your code.
Generally function handles are useful in context of algorithms | | , i.e. sort algorithm needs a comparator etc, integration algorithm needs a value of function at a point (x,y) etc.
Can you rewrite your code to make ' replaceZeroWithNaN2 ' a static method of class ' testClass ' and see what happens? I assume the codegenerator will have a easier time resolving that symbol.