This is the answer I got from the product office:
Currently the system does not allow edit generated line items. A user can enter contract details (type, start date, end date, amount) which the system uses to automatically generate budget line items using the entered contract details (one budget line per contract line); however, these generated line items are read-only.
To support your use case of forecasting when a contract gets paid, you could enter in an Opex line item for that contract that adjusts the payment schedule. For example, if you had a contract for 1/1/16 to 12/31/16 but you did not make your first payment until March you could enter an Opex line item with a negative amount for Jan and Feb to zero out the generated payment amount and add the amount to Mar.
The better long term solution would be an actuals reconciliation feature which is on our IT Planning roadmap