Now that EM Client 7 supports gmail labels. Why don’t you use the gmail label system to create ‘virtual folders’ while only syncing the main all mail folder? Then you don’t have the issue of duplicate emails popping up in search and conversations. I also imagine that it would make the client faster by reducing the local storage requirements and only having to sync one (vs many) folders.
If anything, at least let us search by the new label category tags because that does not work right now.