This option provided for verifying all your purchases has reflected in your Form GSTR2 in GSTN portal. User can mark purchase entry as Unreconciled if your supplier has not uploaded/submitted his sales invoice.
To use this ITC Reconciliation effectively one time Ledger A/c linking should be done in GST Functions Menu >> Set GST type for A/c.
User can do ITC Reconciliation in GST Options/Parameters >> GSTFunctions 1 Menu >> GST Input Credit Info.