A flow assurance system and method includes procedures to query current valve states and determine the likely effect of new valve states on product flow when using an automated pig launcher. The system and method allows for modulating the mainline bypass valve, kicker valve, and isolation valve between fully opened and fully closed states; prevents flow blocking of the pipeline during this modulation; enables new and different, as well as a broader range of, pig launching options for an automatic pig launcher; and integrates with existing automatic pig launchers.