You can’t modify a Filelist, but you can create a new one using a DataTransfer object, and if you wish you can copy your data into it to create a duplicate with the specific change you want to make.
let list = new DataTransfer();
let file = new File(["content"], "filename.jpg");
list.items.add(file);
let myFileList = list.files;
You can then set it as the file attribute of the DOM node:
fileInput.files = myFileList;
If you wished, you could iterate over your old FileList, copying files to the new one.