[jasong]

OmniFocus didn't do it, the operating system did it, and it was designed to work that way.

OF doesn't know what "/Volumes/IOMEGA HDD/" is. When it tries to write to it, the system says "OK, go ahead". The fact that this location was once a removable hard drive doesn't enter into things.

When you try to reconnect your hard drive, the system says "gee, there's already a /Volumes/IOMEGA HDD/; instead of overwriting data, I'll make another location at /Volumes/IOMEGA HDD 1".

The system is trying to do the right thing, and OF is getting caught in the middle.

I would suggest you do backups to a local drive and then use something to sync it over to your external drive.

Or, just use Time Machine.