As you've discovered, exporting as a catalog doesn't preserve the published collections.
The only thing I can think of is to code your publish service so that it can recreate the published collections in the new catalog by communicating with the server. Some of Friedl's publish services have that capability -- see Jeffrey Friedl's Blog » “Publish” in Jeffrey’s Export-to-Flickr Lightroom Plugin
Thank you John.
Humhum ok... You think we can re do the link with the new images in the new catalogue? The ids will not change?
Huumm seems to be a bit hard, but I'll have a look.
I'm not intimately familiar with that part of the SDK. But I think one approach is: In the original catalog, produce a text file containing a description of all the published collections: their name, the full paths of the photos in each collection, and each photo's remoteID and remoteURL. Then import that catalog into the new catalog. Read the description from the text file, calling these methods to recreate the published collections in the new catalog:
publishService:createPublishedCollectionSet (name, parent))
puCollection:addPhotoByRemoteId (photo, remoteID, remoteURL, published)
Alternatively, store the remoteID and remoteURL in custom metadata fields for each photo. Call the server to get the collection sets and collections that need to be recreated, include the list of remoteIDs in each collection. Use the remoteID returned by the server to find the photo in the new catalog.