If any of these files are modified for any specific purpose, if you decide to update the theme after the modification, the said modifications will be overwritten by fresh new files from the update.
That’s what “Any customizations you have made to theme files will be lost” message meant when user tries to update the theme. It’s a warning for users that modify default theme files instead of doing things on a child theme.
You can ignore this if it’s not applicable. 😀
A wise man once said:
"Have you cleared your cache?"