I'm just talking out loud and taking a shot here...
I can't imagine what these two files have in common, other than the fact that they are in the same folder. One of the upper level folders where they reside (the Application Data folder) is hidden, so they would be extremely hard to erase by accident. With that being the case, the problem would seem to lend itself to being possibly an application or registry error.
Not sure how windows literate you are, but since you said that you cleared the registry of all sonar.. files, I suspect you have at least some experience in these matters... Did you look to see if the files were actually still there?... Were you doing something such as deleting the AUD.ini file or any other files when this happened? Does HS4 still work?
These files reside (in HS6) in the C:/Documents and Settings/xxxxx/Application Data/Cakewalk/SONAR Home Studio 6 folder (where xxxxx is the user name you installed the program under). Also, as I mentioned before, the Application Data folder is hidden so you will not be able to see these files in windows explore unless you have the "show hidden files and folders" option checked in Explore under Tools... Folder Options... View... "show hidden files and folders". You could also do a search on the hard drive, but under "more advanced options" you need to be sure that the "Search hidden files and folders" box is checked or you will never find them.
Both of these files are text files and I would have to believe that re-doing the install should have re-installed them. Looking at the Master.ins file on my system it looks like it is pretty generic and the TipOfTheDay.txt file is definately generic, so they could possibly just be recopied back into the proper folder if they were missing... But with that being said I suspect that there is more to it than that...
Deneen
edit).. Rearrange Paragraphs... Grammar