Problem copying / backing up data onto Passport

Here is my problem – i have a few directories (music, work data, photographs) that I back up to my Passport every month or so.  When I first bought my passport the directory I was copying from my PC would be merged into the directory already existing on the passport.  Recently however it just creates a second separate directory with out merging so I have 2 Music directories, 2 Photo directories, etc.  Is there anything short of reformatting the Passport I can do to fix this?

What program are you using to backup your files?

Using Windows 7.