Thank you for your reply, i do sincerely apologise that i haven't replied myself in a while, have been very busy but this is no excuse, forgive me.
Here on the forum it is difficult to advise you when changing Plugin files, as this goes beyond the level of customisation that we can help with, how you changed these files and how this will progress in the future is hard for us to follow.
I understand in your particular case you did this to solve an issue you came across and it wasn't because you wished to, i understand.
It would be better if we could solve the problem's without changing plugin files, however you are unable to provide access to your site at the moment?
As for preventing WP plugin files from updating -
Please understand that i do wish to help, it is just difficult when it comes to altering the source code as we do not provide support for this.
Still wish to help, let me know :)