Alright, thanks for the help guys. I've found a "solution". Hopefully others reading this thread who are experiencing the same problem can also use this solution effectively:
- I had to separate protected OS files. I've set the few files I don't want to be "protected" to have different attributes using CMD, so they aren't considered in that group anymore. Now if I hide protected OS files, they will not become hidden.
- Now I did mention there are some files (normal, not protected OS) I wanted to stay hidden and not be affected when I change things around with other hidden files. Using CMD, I changed these files to be set as "protected OS files", so they now stay hidden independent of the changes I make to "hidden files/folders". I believe this can also be done through the Windows 7 GUI however.
- I set all the other hidden files/folders on my computer to non-hidden. Through Folder Options, I then set it to hide "protected OS files" and show "hidden files/folders". However, there are no files/folders set as hidden. The ones I want hidden are now included in protected OS files. As such, all things I add as "hidden" from this point on will be the only things included in that category, and only those items will be altered when changes to "hidden files/folders" are made.
- Finally, using the right-click context menu trick, I can easily turn these hidden files on/off.
It took awhile... it's not perfect... but it will do. I'd like to thank everyone in this thread for their help. seal, shark, brink, search. You will all be repped!