Reindex Database: If you have 'Use Index' selected in the advanced settings page, this will update the index file used to search your website. 

Skip applies to only this instance of the file or directory. If a directory is marked as 'Skipped' all the files and sub-directories within that directory are 'Skipped' as well. Click 'Skip' button a second time to un-skip the file/directory.

Ignore applies to all instances of that file/directory. If a directory is marked as 'Ignored' all the files and sub-directories within that directory are 'Ignored' as well. However, only that directory is ignored globally. Click 'Ignore' button a second time to un-ignore the file/directory.