No idea.
Changing animation blueprints works fine, even at runtime.
Whatever you are doing must somehow be incorrect, but there really isnt enough info to figure out why.
One thing to check maybe.
The animations and the mesh you use must have the same skeleton for it to work.
Its not an “i think” situation. Either it is the same skeleton and its fine, or it isn’t and it wont work.
There are ways around it, like retargeting, but youd have to look for ways around it to get a valid combo of skeletal mesh + ABP running.