In the Gateway, sets are enabled by default. If you choose to disable sets, this is a permanent change that cannot be undone without contacting OCLC to manually reconfigure and reharvest. Depending upon how your repository is configured, you may have the option of being able to sync your entire repository as a single collection (Entire Repository) or as separate collections (Theses; Dissertations). Keeping the default enable sets may provide both options if you have configured an Entire Repository set. Changing the disable sets N option to Y will provide only the entire-repository-as-single-collection option permanently.
If your repository doesn’t support OAI sets, then the Gateway will enable the “Entire Repository” feature by default.