The embodiments of the present invention provide a method for resolving conflicting changes encountered when reconciling parallel user changes to two synchronized trees of folders and files. According to one embodiment, these conflicts are presented to the user as an interface that requires an indication from the user to the winner of the conflict. According to another embodiment, since certain conflicts cannot be resolved independently, they have to be combined and presented to the user as a single conflict. According to yet another embodiment, after the user has indicated which operations are the winners of all or some of the conflicts, the winning operations are applied to the file tree with which they are in conflict.