FlyMilitary calculates reduced retirement days that were performed in 90 day blocks within a two FY period. Because of this you should not enter orders into the app that are older than Oct 1 of the previous FY. For example, if you enter an active order that qualifies for reduced retirement in FY18 the app will accurately calculate reduced retirement going back to Oct 1, 2017.
If the order was accomplished in FY16 the app logic cannot count those days. To accurately reflect historical totals, you should have MPF total up all of your prior qualifying days and add that number (in days) into the app under the reduced retirement initial settings window (This initial config number should be a multiple of 9 since these days are counted in 90 day blocks). Moving forward the app will accurately calculate your reduced retirement based on orders that are entered under the "Log Active Day" page. Note that you must also remember to turn on the reduced retirement toggle when logging your active orders that qualify.