Hi Bruce,
Just wondering if the non-existing container elements are container elements that were deleted? While most of a workflow is version dependent the container is not, and this can cause problems if the fields are removed from containers between versions.
This can also cause problems if you have existing running workflows when you import your new version, i.e. they may cause the existing workflows to fail.
Certainly non-existing container elements would be a point of confusion and should be removed from the bindings.
Also if you are significantly changing the parameters of a method or using a different method for a task, personally I would opt for creating a new method rather than reuse the old one. Generally adding more parameters is fine - so long as they are optional. Otherwise I would at least consider creating a new method or task and swapping it for the old one in your new workflow version. That's a cleaner approach that is less likely to cause unexpected side effects.
Hope that helps,
Jocelyn