well, maybe you could try leaving your offlines linked, then exit premiere and switch the offlines with the online files... backing up the project file first.
or export an edl, exit, then import into a duplicate project with the files swapped out, never tried that but it would kind of make sense :S
or import ppro project into ae and use the replace command to bring in the onlines. i think this way is most likely to work, but if you've got a lot of time remapping and fx in your project, the import will probably be pretty messed up :/
maybe doing it this way then exporting as a premiere pro project would leave you properly linked up, but i wouldn't bank on your edits/fx being unmolested.