The expert advice we have been receive from the PTC/USER community is to use the "Continue" option in Pro/E
Create one or more workspaces. Check out the the assembly to the first workspace, Modify the assembly to your hearts content in any or all of the other workspaces. Modified objects in a workspace that are not checked out are "inelidgible for upload". Decide which alternative you are going to check in, if it is in the first workspace, check it in. If it is in any of the other workspaces, undo check out from the first workspace, then check out without overriding content in the other workspace. Then check in from the other workspace. A better tango than the import export dance. Your data never leaves the workspace, and you always know what your state is when compared with the commonspace.
Downside is, yes you have to backup the local cache, I think it a small price to pay to acheiveautomatic tracking of modified objects