Hi, Basically GenerateFiles.sh downloads 3 zip archives before compilation and extracts them on top of the checkout. If these files exist already in your Downloads the script just skips them all together.
What you need to do is to check if you have the zip files in your Downloads folder (Files are Optional.zip, Required 1of2.zip and Required 2of2.zip) and re-run the GenerateProjectFiles.sh with the -updatedeps parameter.
If you do not have the files you can get them manually from https://github.com/EpicGames/UnrealEngine and then just extact them on top of the checkout manually.
This was the original problem at least in my case. I hope this helps…