Could a flight engineer fly a jet solo?
You've asked a question the answer to which is in large part a matter of opinion. Also, which three-person cockpit aircraft you're talking about also enters in, as does the stage of flight, as do the conditions at the airport of intended landing. All this, in my opinion, means the answer is "maybe" insofar as an FE who had had flight training be able to get the airplane down safely, and the currency of the FEs piloting would be important as well.

As far as the minimum number of pilots required to safely land a jet with a three-person cockpit (a separate question really), one pilot and the FE can safely land the airplane. In a normal landing, the flying pilot is doing most of the pilot work. The non-flying pilot typically is doing the radio work and manipulating the gear and flap levers at the command of the flying pilot. Since pilots usually trade legs, both are used to doing all that needs to be done. If a non-flying pilot is not there, the flying pilot can easily reach the flap and gear controls, and he's used to manipulating them when acting as the non-flying pilot.

In the scenario of an FE leaving his seat and sitting in a pilot seat and performing the piloting, there is the problem that the FE panel generally cannot be reached from a pilot seat. To a degree, depending on the stage of flight, the FE could pre-set his panel for the landing.

Some years ago I wrote a novel (unpublished) in which I had a single pilot fly a 747. In the novel the pilot had fashioned a wooden pole long enough to reach the FE panel from the captain's seat. The pole had at one end an arrangement that allowed the pilot of manipulate the necessary switches and dials on the FE panel.