So yeah, their plans to escape stymied, the remaining Equestrians all starved to death and the Flemish took over Ponyville. This set in motion a complex series of events culminating in the overthrow of the Equestrian Crown by seaponies, who set in place an industrial revolution in order to pump quadrillions of tons of greenhouse gasses into the air thereby causing runaway global warming, raising the sea lever over nine thousand feet and thus drowning almost all of Equestria and turning it into a haven for seaponies. It did get rid of those pesky humans though.
And hey, when Fluttershy turned back into herself, she certainly had plenty of fish to eat.