That's an unlikely happening.

The program is in Program Files folder and your documents are in your (My) Documents folder. And the install doesn't look at that Documents folder at all. So it's nearly impossible it deletes something there.

Keep searching in Explorer (and in the Recycle Bin) for your files (search by name or extension or last change date, whatever is the easiest for you). If they really are gone, you don't have anything else than the last version that's on your backup.

Kees