When you swap syringe in a Spawner, the amount of items of each type stays, so you can bypass the need of mob-specific items. For example, if I place a Skeleton syringe, inject three bones, then swap the syringe with a Wither one, the Spawner will have three nether stars stored for spawn.

Simply left clicking the current syringe with the new one in the spawner GUI.

Fixed next release

I cannot reproduce this. How exactly are you doing this? How are you swapping the syringe?