My Xero Invoice Does Not Match Function Tracker

When connected to Xero, you should never edit the invoice directly in Xero. The changes you make to line items will not sync back into Function Tracker,

If you have not taken payment, then from within Function Tracker, click on the Refresh Invoice icon to send the Invoice to Xero again.

If you have taken payment, you will have to first delete the payment from within Function Tracker, this will then void the Xero payment and unlock the Xero invoice. You can then re-apply the payment after you refresh the invoice, but this could change reconciliation dates in Xero.