I modified the methods Search and Download methods (Folder.cs) to accept and pass on the extra skip parameter, but i think you could definitely use this to download the ids and then pass then to Download yourself.
folder.Download(SearchMessageIds(query: "ALL", skip: pagenr*perpage, count: perpage))
folder.Download(SearchMessageIds(query: "ALL", skip: pagenr*perpage, count: perpage))