It will need to be aligned with the axis of rotation. OK this is not a bug report really. I think your handlebar was being associated with the rear wheel, so it disappeared when the rear wheel was off screen.
It's technical assistance, so I'll move these posts after a while.
I have some advice about bikes:
1) Rear suspension
I recommend the "trailing arm" suspension type for the rear suspension. You create a "trailing arm" object with its object centre at the pivot point for the rear suspension. That must correspond with a "lower pivot" point in the vehicle editor.
2) Front suspension
You can find that the lower fork leg (mudguard or 'brake' object) does not rotate correctly with the upper fork legs (handlebar or steering wheel objects). This is usually the case when your first set up the front suspension. When you steer, the stanchions appear to become separated from the lower fork leg.
To fix this you need to do two things.
1) Adjust the "steering wheel" (handlebar) object so that the rotation point is in the right place (aligned with the top bolt - the centre of the top bolt should have x=0 and y=0).
After the "steering wheel" is in the right place, then back in the vehicle editor:
2) Increase the "Trail Reduction" in the "Steering / Driver" section to match the offset between the stanchions and the steering axis. As you do that, the wheel moves forward. So then you reduce the "Forward" value in "Suspension" section by the same amount to compensate. By trial and error you can end up with the steering axis line going straight through the centre of the bolt, then the steering should work correctly.