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What is the theme you are using and what are the changes you would like to make with a child theme?
You mentioned making changes to the theme - are these changes that you have made to the main theme?
How did you make the changes? Did you make them directly in the theme template files? If so, those changes are the ones that would be overwritten on an upgrade. So if that's the case, hold off on any upgrades until we get.this sorted out.
Yes, that is correct. The changes can be done in the child theme. So, here are the things that need to be done.
We need to identify all changes made.
Migrate those changes to a child theme.
BUT, from what I see here, you were AWESOME in documenting the changes you made. And although you may have changed a thousand lines of code, we know exactly how to back those out AND we know what code you need to get the results you want.
Same with the plugin. That may be a little more difficult to deal with, but a customized plugin is manageable. Sometimes it is also necessary. We can look into that specific plugin to see if it has hooks into the theme and if we can change it externally. Again, we know exactly what you changed, which is most of the battle.
Are these the only two major changes that you made? If so, you are in much, much better shape than I thought from reading your original question.
Re-reading things... it sounds like you made other changes. But if your documentation is as good as these two, it's more work, but it is doable. The most difficult thing in the whole process is knowing what changed because anything we don't know about will break. If you have notes about everything that changed, we can prevent it from breaking.