On a more in depth look, it appears that the variables do not affect each other, but both affect the variable on the page. I am able to delete one without getting rid of the reference, leaving me with one functional variable. It's a pain, but at least it can be manually fixed. My previous question still remains though. Does anyone know what would have caused this?
If I were in your shoes I might try the following.
Make a backup copy of your RoboHelp project for Justin.
Enable the option to clear the CPD when RoboHelp opens.
Right-click a file in the Project Explorer pod and choose to Explore. (This should open Windows Explorer)
Close the project.
From Windows Explorer, locate the file named RHVar.apj. Right-click that file and open it using Windows Notepad.
Are all the variables repeated in this file? If so, clear the duplicates and close and save the file.
Restart RoboHelp and see if things are back to normal.