[Newbies] still don't understand how to get rid of obsolete classes and bad references

I have been messing around with the obsolete classes in my image and no matter how many times I Garbage collect , set things to nul, clear command histories and numbers of other things I have tried they don't go away. I have read the cleaning up junk article on the wiki along with others.

From what I understand the classes stick around because something is

referencing them. How ever when I find an object that is referencing the obsolete class and set that reference to nul, accept the changes it seems like it just comes back later. Am I supposed to set it to nil from something other than an inspector. Why can't I see the obsolete classes in the system browser.