It depends on, among other things, the number of people already in your tree.
What you can do is export a gedcom without sources and then upload that to start a new tree.
On the new tree I suggest you forget about all links/hints that are to other trees and deal only with documents. Never add a hint to your tree until you are sure it applies to teh person you are documenting and never add more than one person at a time ( don't add entire families from census, etc.)
Yes- it will take a bit longer but that way you are sure not to get duplicates. Never-ever- enter a person more than once. Once entered you can always select them from the list of people in your tree to add as a wife, child, etc. to another person.