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Eric,
I haven't use the config.pro option Gerald was talking about, but you could make a separate batch file to launch your different Pro/E configurations. Within the batch file, before you launch Pro/E, include the command "SET PTC_WF_ROOT=<absolute path=" where=" you=" want=" to=" cache=" your=" windchill=" session=">". I believe that the server information is stored in the cache defined by the "SET PTC_WF_ROOT" environment variable. So then you'd have a short cut to launch WF4 w/ PDMLink server and one for WF3 w/o PDMLink server (since you won't register one).
Willy Chung