Is it possible to edit a mesh between frames, so that the animation is playing, and at one point, say, a few verticies move around. I hope that makes sense.
You can deform a mesh with either an Armature object, or with ShapeKeys (probably … maybe what you had in mind)
Note: ’ Adding or deleting a vertex once shape keys have been added is very tricky. The changes are propagated to the other shapes based on their position in the current shape, this can have drastic effects on other shapes.
If this is the problem, then try Propagate To All Shapes, see post #5 for workflow.