You can find the file wau stores you preferences and set the value there. WAU saves the toc version it last detected, and continues to use that until it finds a new one.
WAU is no longer maintained. You will need to work around this issue yourself.
Ahh HAH! Eureka!
Thanks Sylvanaar, that is what I was looking for. I had tried to find the WAU files once before to no avail, but after reading your last I had the brilliant idea (duh) to not update anything today except for a preference setting, then do a search on all files including hidden ones to see what was saved with today's date. I found the WAU config file, opened with Word, and changed the TOC to 20400.
Started WAU again and TADA, everything is working correctly. Now, only the files last updated a week or more ago (or the files that got updated but the author forgot to change his TOC) have the strikethroughs.