PDMLink works a little differently than Intralink did.
Here is what works for us for similar situations. When the top level assembly is saved, all the other stuff that Pro/E thinks is changed will pop-up with an option to check them all out - instead of checking them out, change the option to "continue" for the objects that were not intentionaly changed. This will make the objects as "modified but not eligable for upload" in the workspace. When the assembly is uploaded or checked in, PDMLink will ignore the objects that are not elligable. The modified objects do not need to be added back to the workspaceas was previously required in Intralink.
In PDMLink, objects have a default "view only" status unless they are specifically checked out.
In Reply to Robert Balkevitch:
With Windchill, When ever i set lower level items to Lock or Read Only, My top level assembly that i am trying to save will not save. The only thing i can think to do is to let everything save( down levels that regen, instances and what not), then go update the down level items before i can check in my top level.
