It certainly is possible that removing a choke will reduce common
mode current, depending on where it is placed in the feedline, along
with the various line lengths and ground connections. So if the
noise is being picked up via common mode current, that would reduce
the noise level.
Here is an example: suppose the coax is 1/4 wavelength from the
antenna to a well-grounded station. Because one end of the coax
shield is grounded and the coax is 1/4 wavelength, the shield will
look like an open circuit at the feedpoint, and there will be little
common mode current.
Now insert a choke at the radio. With a perfect common mode
choke the shield now looks like a quarter wave open at the far
end, which will have a low impedance and a significant amount
of common mode current can flow on it.
That is simply an example that such a condition is possible.
Whether or not that is the explanation for the specific behavior
in your case depends on a lot of other factors.