Atlas upgrade issue

Hi all. I am currently in the process of upgrading an application from 8.18.24 to 9.12.5. I have opened the application in the new version and sorted all Java errors.   I am now in the process of upgrading from Atlas 2 to 3 however during the stage where you download Atlas Core and replace the existing Atlas UI Resources. The file is not being overwritten. I have also renamed Atlas UI Resources to Atlas Core as instructed in   I have also tried downloading Atlas Web content but that is not showing in the file directory as it should.    Comparing it to other applications currently being upgraded this does not seem to be an issue for them so I am confused to what is causing this error?   Would anyone have an idea as to why this is happening and how to resolve it?  
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