If your project contains conflicts after updating from the Team Server, these conflicts will be listed in the 'Changes' dock. This dock contains one row for each project-level item (project, module, folder or document) that is changed or conflicted locally.
If you select a row that is about a conflict, you should be able to select the 'Resolve using my/their document' items in the 'Tasks' drop-down menu of the 'Changes' dock. You can only select these items when you are at the project level of the dock, not when you're looking at the details of the changes in a document. In other words, the dock should indicate that the location is 'Project'.
Mendix 3.0 is still RC1 and not perfect. File an issue in the support site and describe the followed scenario as precise as possible.