On my RT3 system, I use one directory with my name as its title. This directory seems to store all my phone contacts and NAV DIRECTORY entries together in a single 'file'. However, the RT3 seems to use the term 'file' to mean a single entry in a 'directory'. Also, the NAV directory seems to select destinations from the USER directory and ignores phone number entries.
If you select the DIRECTORY functions and CONSULT your USER directory you should find several entries for HOME. Use the DELETE FILE option to erase the entries you don't want. When you go back to the NAV function, and look in the SELECT DESTINATION\DIRECTORY it should only have the HOME entry you want. For this to work you will need to check that there are no entries for HOME in the other USER directories (USER1, USER2, USER3, USER4). I only use the USER1 directory, the title of which I have changed to my name.
I use the ARCHIVE function to put any entries in my RECENT DESTINATIONS folder, which I want to re-use, into my user directory. I have not yet found a way to delete an entry from the RECENT DESTINATIONS folder but have not found this to be a problem.
Hope this helps.