Does deleting pages in panels, delete all the code that was created usin that page in Panel?

I'm not sure I understand what you mean. My best guess is (for now):

I'm putting code into custom content panes inside a panel. If I delete a panel, can I still keep the code I put in the custom content pane?

If I'm remotely right, there are two answers to your question:

1. Don't put code in content panes unless you really really have to. PHP code in configuration is insecure, slow and difficult to version control.
2. In Panels 3.7 you can create custom content panes that are independent of the panel(s) they are embedded in. You can activate the function by checking the 'make this content reusable' box.

Please write a clarifying comment I'm completely smoking crack here. If you write what you have done and what you want to achieve it will be easier to give sensible answers.

Cheers!
//Johan Falk, NodeOne, Sweden