I do not know the inner workings of the Content Paradise store. All I know is that I uploaded the new files to the correct location ensuring that new over wrote existing. On some I think I even deleted the existing before uploading the new.

If you have used up all your downloads, yes, you'll need to contact the CP store to get them reset. However my email giving update details contained a list of all the links to the files on my own server so if there was an issue you could have used those without any problem.

I'm not sure that I follow. Are you saying that you have not been able to get your downloads yet?