You don't have to delete your whole library in order to track your progress correctly, you could archive everything you have now under a collection named "Archive" and then use a new "Disseratation" collection for the current research.
However, a clean start to Zotero depends on whether you use it locally or sycning with an account.
If you are using it locally, easiest way would be choosing to wipe all data during the uninstallation process and then reinstalling Zotero freshly.
If you are using it with an account, you should select all your collections one by one, right click and choose "Delete Collection and Items" everytime. Then you should delete remaining items in the view which you see when "My Library" is selected. Finally, you should right click on "Trash" collection and then empty it.