Try doing a Save As and save your project under a new file name in a new location.
It could be that, in the process of tinkering with the directory and file names, you invalidated a link.
And, of course, if you changed the names of any Program Files or Program Data folders, you may have really broken something and you may need to uninstall, run a registry cleaner and reinstall. It's not clear of that's what you mean when you say you changed the names of "production support files" -- but, if so, that's never a good idea.
Contributory things to put on your troubleshooting list
What version of Premiere Elements and on what computer operating system is it running?
Assuming Premiere Elements 12/12.1 or 13/13.1 on Windows 7, 8, or 8.1 64 bit -
Sounds like you have at least two things going on, as you have been pointed to, relating to when you start changing things after a project has been saved closed, but you seem to be focused on Auto Smart Tone. It may be a band-aid in a more complex matter, but have you hit the "Clean Auto Smart Tone Learning" button at the bottom of Edit Menu/Preferences/General? And, have you deleted the Adobe Premiere Elements Prefs file under Local Disk C\Users\Owner\AppData\Roaming\Adobe\Premiere Elements\version number\. Make sure you are not working with hidden files and folders which prevent you from seeing the path to the Adobe Premiere Elements Prefs file.
I tried your idea of copying the project to another directory and that did not fix the AUTO
TONE breakdown. The renaming of the directory with the prel file caused the malfunction of
the AUTO TONE function and nothing I did was able to restore it. I assume that the AUTO
TONE function code is sensitive to directory naming and this is a weakness of version
Premier Elements 12.
I may be time for me to upgrade to PRO.