The game already tracks the players which are involved in FATE (assigning rewards at the end). These same metrics could be used to adjust the FATE difficulty at set time intervals during the FATEs existence.
For mob type FATEs, after the interval adjustment, the HP of new spawns would reflect the new difficulty.
For boss type FATEs, an actual change to bosses HP would have be performed mid stream.
For delivery FATEs, is this ever an issue? Those always seem to be about 20ish items and done.