Did you perhaps switch from Windows to Mac?
With Settings/System Settings/USB Mode at Auto Detect, the Sansa chooses MTP mode when connected to any computer running Windows Media Player 10 or above. MTP mode does not do Refreshing Your Media.
Connected to a Mac, it goes to MSC mode, which is the basic USB connection, and MSC mode does Refresh every time you change something–or, sometimes, even click on a file while connected.
But the Mac doesn’t have WMP–Apple vs. Windows–and you need to use MSC mode to connect to it.
It’s also possible you switched to a Windows computer still using WMP 9 or below. Windows XP came with WMP 9. In that case all you have to do is go to support.microsoft.com and update Windows Media Player.
If you really hate the refresh and feel comfortable with computers, you could install the alternative Rockbox firmware on the Clip. It does its refreshing in the background. But you do have to follow its install directions carefully and you need a little bit of a geek streak to love Rockbox.