QuickBooks has a handy feature showing you the most recent company files you've opened.
Unfortunately, once you've move a company file to a new location and open it, you'll now see the same company listed twice in the Open Company dialog box. Not to worry, this is easy to fix altough a bit buried.
First, open any company file. Once the company file is open, then select the File menu, choose Open Previous Company and you'll see an extra menu option Set Number of Previous Companies…
Set this option to 1. Now quit QuickBooks and reload it. Now you'll see only the company you just opened. The list is now cleaned up.
Got more than one company file? No problem. Just leave the previous companies setting to 1 and open each other company one-at-a-time. Be sure to quit QuickBooks after you open each one.
On the last company file, change the previous companies value to however many companies you have. Now the list will show only the ones you've recently opened. Since these are your valid company files, you're done!
I recall there being an easier way to do this, something with a file in the C:\Windows folder. But I couldn't find it, so I suspect that involved older versions of QB. QB has to be storing it somewhere though, so there's gotta be an easier way.