You would need tp copy the new dlls into place and then register them. I am not sure about the unregister part. I do not think it is needed, but it is possible that if you do not there may be some let over clutter in the registery. I do not think it would be a problem even if it is left behind though.

The other issues you may run into is file in use requiring it to be copied as part of the bootstrap and of course the user not having access to copy files into this location.