Do you have the output from the patch command? It should have changed the code as needed.
In any case, I tend to use the full package upgrade, even on modified installations. Patches can’t include binary files, like images, so a successful application of the patch upgrade process will occasionally miss binaries. If you generate a .diff file by comparing your modified installation to the stock 2.4.5, then try applying that patch to your new codebase, you’ll preserve modifications.
(For our own hosting at SFU, we’ve gone one step further and are using git to manage production installations. This permits a lot of flexibility when managing modified installations. But git can be a big learning curve too.)
Public Knowledge Project Team