Here is a new thread with some tips and suggestions on how to use the new forward/back annotation in Multisim and Ultiboard v11. In previous versions (v10.1 and earlier), changing a shape in Ultiboard and then back annotating would likely cause the part to get removed in Multisim.
Although it is still advised in most situations to adjust footprint mappings in Multisim first and then forward annotate, the back annotation (Ultiboard to Multisim) with a part change has been improved and will reduce the likelihood that parts will get removed. The user still needs to make symbol to footprint changes with care, so as to not produce a bad PCB design, but with the proper knowledge, Ultiboard users should find this much improved.
Here is a short PDF guide to walk Multisim/Ultiboard PCB prototyping designers through the process of Back Annotation with a footprint change.
