The manifest files you are referring to are only used for distribution by the launcher.
They are only used by the launcher to help download the content and repair any corruptions during download. The launcher needs the manifest file for a piece of content to recognize what the content is. So removing the manifest will likely make the launcher think the item was never installed.
The manifests are never copied into your project, but are instead included next to what is effectively a “holding tank” of files the launcher clones from when asked to install a piece of content into a specific project/engine.
If you are prepping content for the UE marketplace you don’t need to worry about the manifest file as we’ll add one when we prep your content for distribution.
I hope that clears some things up.