How is an emboli able to traverse a patent foramen ovale if the net flow of blood is from left to right atrium?

Possible. The heart is a pump and a dynamic process. The net pressure is from high to low. But invariably with activity motion and changing in position the flow can switch transiently. If a clot is in the flow at that time then it can become an arterial emboli with all its consequences.
Paradox. This does seem to be a paradox but while the net flow is in the opposite direction there is some flow from right to left. If the clot is near there at just the right time it goes troug.