Index allows you to visualize the contents of your Folders and sub-Folders. As data comes into your Folders, that data is indexed for Index so the data can be almost immediately visible. Re-indexing wipes the slate clean (the index of your data in the Folders) and re-indexes the contents of your Folders for Index.
How long re-indexing takes depends on how much data and how many Folders are being re-indexed. Re-indexing Folders with a huge amount of data can take hours.