For anyone interested in this topic I believe I figured out why this is happening. I found that clearing the Saved Passwords check box for Internet Explorer as well as clearing the Saved Passwords check box for Edge stops CCleaner from clearing any saved passwords in Edge. If anyone from Piriform reads this maybe consider correcting this in an upcoming update.
I have noticed that when I run CCleaner it clears all of the saved passwords in Microsoft Edge. In CCleaner I have every Edge option box unchecked yet it still continues to delete my saved passwords. This happens on multiple computers running Windows 7 and Windows 10 with all updates installed. This has been happening for some time now and is still an issue (for me anyhow) with the latest version of CCleaner 5.48. Is there a way to correct this problem? Thank for any help or guidance you can provide.