If I import existing files, will links be broken

I know you don't place files in actual, physical folders and subfolders, and that you're just using a custom taxonomy, as you explain here: https://www.joomunited.com/support/faq/wp-media-folder/does-wp-media-folder-create-physical-folders-for-your-media

But my question is this...if I am converting an existing HTML site over to WordPress, and I import hundreds of pdf files from their physical folders/subfolders via WP Media Folder, what happens to the all the links to the files in the pages I've imported into WP? Are they all going to be broken? Will WP Media Folder essentially search/replace links or will I need to do that separately/manually? Thank you.