When you are in USD composer, and you want to save a USD as a flattened file, just use the command, “save as” with the flattened option. This should produce one larger USD file with all the USD assets in there. However, remember, it will not include the textures. Those are still in a separate folder. You also have the “collect” command which does collect everything needed into one place.
Having said this I do not see your reason for having to flatten your file in the first place. You can make a file in composer and open it in Issac Sim without needing to flatten anything.
Also you can just skip usd composer altogether and just make the scene directly in Isaac Sim.
If you are moving the file from one Omniverse set up to another, make sure that both of them are fully logged in and on the internet.