The only way to solve this is to split off your updates. That is, have one last update at your current download location (let's call it http://example.com/updates/%file% ) where the only change is making your app call wyUpdate with the new basedir and including a new client.wyc file with a new download ite.
The new download site will be http://example.com/new-updates/%file% . This way your old users get updated to an intermediate version and from there can get update to the latest version. And from now on you'll be uploading your updates to "new-updates" on your server (while leaving the old "updates" folder as a way for your old vustomers to step into the latest release "branch").
Does that make sense?