Are you saying your "Homebase" shows 2 files. Which "Homebase" are you in?.

If you have the ALL TAX RETURNS homebase open and have transferred both Organizer and Individual files they will both show up.

Possible you could have imported your client files from another folder or drive (or resaved them to), and now Homebase is showing 2 files per?  

Under HomeBase View, select All Tax Returns and look at the full path and file name column.  This will tell you where ProSeries is reading from.

What Year ProSeries?

Does one show something like C:\prowin21\21data\filename1.21I and the other one shows E:\prowin21\21data\filename1.21I ?