I can't imagine them changing from Zero-keel as they would have to alter the aerodynamics of the car at the front as it has been designed around Zero-keel.
There's a lot that can be done by just subtle changes to the suspension geometry. Maybe move the front wheelbase forward or backwards, just a few millimeters could make a difference. The suspension is rising rate, that could be altered by slight geometry changes.
You don't need massive changes in the middle of the season, What I see are subtle alterations to the geometry to suit the driver's preference.
Kimi has done some spectacular passes in the braking zone, he has also had problems of the inside wheel locks up. The McLaren engineers could be fine-tuning his car for just that specific set of circumstances.
The suspension problems are likely the result of the compromised geometry of the zero-keel. They are probably revising the suspension to correct some fundamental flaws like the pushrod angle relative to the wishbone axis. I also think the droop in the suspension can make for an ugly camber curve unless you're running a Long Short Arm design, rather than the more common Short Long Arm. The problem is, will we be able to detect the changes visually?
Fortunately, the TF106B's suspension update is a bit obvious, I wonder if we'll see Maclaren raise the rockers as dramatically as Toyota did. Why isn't the Toyota B car out for Nurburgring?