I believe the only way to fix this is to go back over the procedure you followed when you first adjusted the zero beat point, and then do it again. Please forgive my being so detailed and pedantic, but due to the nature of the circuit, I’m afraid it will be very, very touchy to tune to zero beat. What I’m attempting to present below is a procedure that i hope will allow you to make this adjustment in a repeatable, and predictable manner. Otherwise, you’re libel to go running screaming into the night!
With that being said, please understand that I’ve never done this on a theremin. However, I have done similar adjustments on radio gear, so this information applies here as well.
The Tuning and Testing instructions in the field upgrade manual say to install the theremin on a mic stand (away from everything else in the room, BTW…), set the pitch tuning control to the 9:00 position, and proceed to adjust L6 so that you’re at zero beat when your body is at arms length from the vertical antenna. It is very important to set the pitch tuning control to 9:00 before proceeding, for reasons I’ll explain later.
So, the procedure will be to tweak L6, remove your hand and plastic tuning tool from the unit, stand with the right side of your body an arms length from the antenna while you are squarely facing the theremin (like you’re about to play it), and then see how close you got to zero beat. I don’t believe you’ll be able to directly adjust to zero beat while you’re adjusting L6, because your hand is likely to be adding capacitance to the circuit while it is in the vicinity of L6. Therefore, you’ll need to adjust L6, remove your hand, assume the playing position, and then see how close you got. You’ll probably go back and forth like that several times before you zero beat at the playing position. Please remember that not only do you want to adjust for zero beat, but to also be able to change the pitch smoothly with your hand when moving it towards the pitch antenna, so you’ll need to find the happy medium between these two goals!
After you’ve achieved zero beat, then put the cover on with all of the screws, set the pitch tuning control to the 12:00 position, and then see if you are still at zero beat when in the playing position. Please be aware that readjusting the pitch tuning control is very important because the offset from the 9:00 position to the 12:00 position is probably to compensate for the capacitance introduced by the cover. This is why it was important to set it to 9:00 before beginning to tune the zero beat point.
Be patient! Remember what direction you’ve turned the screw on L6, and how far you’ve turned it (use tape to make a little flag on the tuning tool so you can see how far you’re turning it), and use a plastic tuning tool to adjust L6, not a metal screwdriver. Also, always make small adjustments on L6. Sneak up on zero beat! It can be easy to adjust L6 too far, and drive yourself crazy going back and forth because you keep tuning past the zero point!
Once again, I am no expert when it comes to tuning theremins. However, I was a radio tech years ago and the concept of tuning an inductive/capacitive circuit is really not all that different. However, since the theremin’s circuit is meant to be interactive with your body’s capacitance, tuning this circuit is probably a lot more touchy than tuning a local oscillator or an IF strip.
Have fun with it, this is all part of the experience of doing it yourself!

Hope this helps,
Bob