When I use proxies for high-res footage and am finished editing, I delete the proxies and so everything becomes offline. But just highlight all of the offline footage in the project panel, right-click, select “Link Media,” and select the file and Premiere should automatically (if everything’s in the same folder) restore all of the offline footage.
I’ve never used Encore and don’t know the specifics on your project so maybe this is bad advice, but have you considered just exporting a high-res video through Premiere rather than linking your entire project to Encore?
Hope this helps.