You need to provide more information.
Not equalizing the levels would mean the pressure outside did not equal the pressure inside when the system was closed. A higher level inside would mean a lower pressure in the system compared to atmospheric pressure.
If you are measuring only the change in volume of this system, this would have no effect on the results (as pressure remains constant, it does not matter what the pressure value actually is).
If you are performing a calculation where the pressure of the system is included and you are using atmospheric pressure as this value, then a systematic error may be introduced by not equalizing. How this would affect the value of whatever Y is depends on the calculation and the initial conditions.