The simple answers to the questions, as others have pointed out already, are that Jones got hurt and seems to have struggled to grasp the scheme.
There's something else I want to highlight regarding his athleticism. While Jones is correctly known to be a great athlete, there is a hole in his profile.
At the combine, he ran a 4.41 (93rd%), jumped a 132" broad (96th%), and a 37.5" vertical (76th%) at 6'1" 220 lbs. Those are the numbers that won him his reputation as a freak athlete. And rightly so, to an extent. But you'll notice these are speed/explosion metrics. He didn't do the drills that more effectively measure change of direction and agility (3 cone, short shuttle) at the combine, which always makes me raise an eyebrow, because often players skip the drills that they're more worried about. He didn't do those until his pro day and the results were less than ideal.
His 4.40 short shuttle places him in the 10th percentile, and his 7.05 three cone in the 34th. Metrics don't bear out in the league 100% of the time, but I think they're good indicators of a players' ability and they fit in Jones' case.
Jones has looked to me like a straight line athlete who struggles to change directions. He's more equipped to be an undersized linebacker than a big safety. But Gutekunst drafted Burks for that linebacker position, which leaves Jones out in the cold a little bit. It should be mentioned that while Burks is considerably slower in a straight line, he's quite a bit more agile than Jones which might be why he quickly won a role before getting hurt.
Lastly, Pettine values intelligence and schematic comprehension more than most DC's. Whitehead is playing because he understands the concepts on the field. Jim Leonard made his living in the NFL following Rex and Mike and knowing the scheme inside and out. If Jones isn't grasping the system, all that speed is useless to his coaches.