When either Discovery or an interactive Web Part analysis is run, document libraries are searched for Web Part Pages from which Web Parts are collected. Because this can be a resource-intensive process, by default only document libraries that have 50 items or fewer are searched. ControlPoint Application Administrators can, however, specify a different threshold by changing the Value of the ControlPoint Setting Maximum Size of Library in Which to Search for Web Part Pages.
Note that, at a higher threshold, more Web Part Pages will be searched, but the process will become more resource-intensive.
NOTE: If you want to include all document libraries in your search, regardless of size, set the threshold to 0.