In the file system, there are actually .new files for most of the files mentioned in modified.txt. For the files mentioned but without corresponding .new versions, I'm not sure if they've been overwritten by Update.exe already, or perhaps they were meant to be deleted and so there is no .new equivalent.
I haven't been able to run the site yet for unrelated reasons. It almost certainly wouldn't run without me merging in all the .new files. Are you suggesting that I leave the questionable files in place, and otherwise follow through with the upgrade process? For now I'm going to revert the database and files, and then try again.