As tables are compared, Replicator writes down all encountered differences in a temporary file. If you expect a lot of data (especially if you enable logging of same record data), specify a folder on a large drive here.
Whenever you save a project, we write down the list of selected tables. If you deselect a table, you will want it not to be compared (nor replicated). When project is run, if a new table is detected - it will be skipped. Change that behavior with this option.