Hi there, not a problem! This is normal when upgrading themes.
The first issue is up to you how you handle. Meaning it literally will tell you which chunk of code to use. If you didn't edit anything in that chunk that you see, just revert. If you did, press use custom. Or you can merge them together use a diff program (I use winmerge).
The second issue is caused when XenForo doesn't really know (either through bug or something edited, Ive never understood) what to do with the new code vs the old so you actually need a merge tool. You take the custom footer code and copy it to the winmerge program (Id also save it as a .txt file on your desktop as a backup). You then revert that template, take that new footer code, and then compare it to your custom. Merge changes, and bring it back in.
Another option, though one I do not endorse, is to just save the templates and see if anything broke. Often times these messages are because XenForo changes a right to left phrase or some javascript or meta data change.
We do have a premium upgrade service if you would like, PM me for details!