Basically the title

In my case I also set permissions = "644" to allow the file to be edited, however the clobber occurs without permissions being set.

Reproducible with the following config

hjem.linker = pkgs.smfh;
hjem.users.<name>.files = {
  "example" = {
    text = "Example text";
    clobber = false;
    type = "copy";
    permissions = "644";
  };
};

rebuild, edit the file, rebuild again, observe its content being reset to Example text