I can't say what happened exactly to your code during the upgrade, as it seems the custom code has been converted into standard or something like that. It's more a bug than a feature.
I think it's best to install relevant all SAP notes which could apply to the enhancement Framework.
After that, put aside your custom code, retrieve the standard version (in version management), and reapply the modifications.
I'm not sure for best practices. I would just opt for ENHANCEMENT-POINT instead of ENHANCEMENT-SECTION, and create an implementation of the point. The ENHANCEMENT-SECTION is to use when you want to have a default code, and allow other developer teams to overwrite the default behavior. Anyway, it doesn't make a big difference.
About removing the "enhancement area": you cannot "undo the implementation" because it's not an implementation; ENHANCEMENT-SECTION is just a place where you can create an implementation. To remove the code, you must do it in the classic way, you don't need the spiral. The spiral is for working with enhancement implementations. ENHANCEMENT-POINT and ENHANCEMENT-SECTION are just places ("enhancement options") for adding an enhancement implementation. In the classic way, a standard ABAP source can be modified only if there's a valid modification key. But, as I said previously, try first to retrieve the standard version, and recreate the implementation (at that time, you'll need the modification key anyway).
