Did you really expect anything else? Files are protected with digital signatures and if you change the contents it will corrupt them. This is by design as a provider may wish to add copyright messages and not want them taken out. If you desire more functionality in purchased code, you should contact the provider to request this, even if you are able also to add it yourself. The feedback loop from customers back to software developers is essential for products to move forwards, and it hurts product development when it is bypassed by people making their own changes that more than likely will not get contributed back to the product developers. To avoid corrupting the files, add functionality in files outside of the protected component, and also raise an issue with the developers if you feel that they have protected too much of the software so as to not make it flexible enough.
Disclosure: I am associated with ionCube.