Hello,
sorry for the late reply. In the PDF24 Toolbox, Save asks for a folder when there are several results and saves every file there under its original name. Existing files are never overwritten: if a file with the same name already exists in that folder (for example the original files, because the folder dialog opens in their folder), PDF24 adds " (1)" to the name.
So if you select another, empty folder, all protected files keep their original names. Replacing the original files directly is not possible at the moment; this is on our to-do list.
Protecting PDFs also works online: https://tools.pdf24.org/en/lock-pdf