Is there a jumper on the Amiga 2000 like on the A4000 that allows you to "lock" the computer into either NTSC or PAL?
It depends on the Agnus revision.
OCS Agnus was fixed to 50 or 60hz and couldn't be changed ever.
Some ECS Agnus detected 50 or 60hz through a pin, but on some ECS Agnus that pin was used for something else and the 50 or 60hz default was internally set but could be overridden by software.
I'm sure there is a commodore service bulletin online that covers what needs to be done to replace one Agnus with another and the details about the different Agnus were in there. It's possible that the decision to revert to specific Agnus chips may have been as a result of the extra work required when servicing old motherboards that didn't have the 50/60hz jumper.