You can do some tricks to fullfill your target:
1. the project file is an XML. You can reimport the schema in a new project file and copy over the layouts from one XML in the other. During the import get rid of the outofmemory exception by not importing the procedures.
2. If you select all / some tables in the layout or tree you have a option 'Refresh' which should do the synchronization only for the selected tables. Usually the synchronization would import again all tables, which will lead to out of memory problems. But doing so you will again not import all objects.
Hope this will help,