It seems you want to copy the files from your GitHub Repo/Azure Blob Storage to Azure VMSS and the VMSS is configured with autoscaling, which means you want the copy files in all the instances, including the autoscaling instances.
If I'm right, then manually copy files is not the right way. You should know all the instances of the VMSS are created from the configuration that you set in the creation time. If you just copy files to the existing instances, then when it auto-scales, the new instances will not have the copy files. There are two ways for you.
One is that you can create a custom VM image and copy files in that image. Then use this VM image to create your VMSS.
Another one is that if you use the Azure File Share, you can mount the file share to the VMSS, then all the files in the file share will exist in all the instances of the VMSS. Here is an example.