The reverse of this question was asked when only the Panda Flight I {Burke} and the Flight II {Cole} kits were available and modelers wanted to build a Flight IIa. It is not as simple as slapping on (or in your case removing) a helicopter deck and hangar.
Yes the stacks were changed in later Flt IIa ships, plus the mine hunting gear hangar was added. These need to be changed. Also in the change from Flight I/II to IIa the aft face of the bridgehouse was raised to increase the clear field of view for the SPY-1 radar panels. They need to come down about 1 deck level. Fore & aft there were CIWS guns. The later ships have Rolling Airframe Missile launchers in their places. The aft Vertical Launch System cells also changed shape, location, and number of cells going from the I/II to the IIa ships. The latest units have a different forward gun also.
Backdating a late Flight IIa Burke to a Flight I or II ship is a serious undertaking. You may be better served finding a Panda Burke or Cole. Fortunately the differences between a Flight I and Flight II are largely internal and electronics