There are two main types of conflict. The better known where file content is in conflict requiring an invocation of the file merge tool. The lesser well known where actions conflict but not file content. For instance, where the file was modified locally yet deleted in the repository, or the file was renamed from "a" to "b" locally, but from "a" to "c" in the repository. In such cases, merge may not be not possible, and the user must decide which change to accept, "use local" or "use repository".
The Synchronize wizard recognizes certain situations that are identified as pseudo-conflicts. For example two users may have independently deleted the same file or created the same folder. These are situations that you might wish to investigate, but if you accept them in the Synchronize wizard, the metadata will be updated so that they do not subsequently appear again.