In Windows Explorer, right click on the drive Divinity is installed to and select Properties; then on the Tools tab select Error-checking.
When the games saves over an existing save, it does so to a temporary folder first (in case there are any problems during the save), then deletes the old folder and re-names the new. This would not cause any permanent extra disk usage, though. As the saved games get larger (as you enter new areas, etc.), the files saved in the dynamics folder will also become larger, but this would not account for 20MB per save.