ADDITIONAL SYSTEM INFORMATION :
$ java -version
openjdk version "21.0.2" 2024-01-16
OpenJDK Runtime Environment (build 21.0.2+13-Ubuntu-122.04.1)
OpenJDK 64-Bit Server VM (build 21.0.2+13-Ubuntu-122.04.1, mixed mode, sharing)

A DESCRIPTION OF THE PROBLEM :
If the argument of Files.setLastModifiedTime(file.toPath(), FileTime.fromMillis(millis)) is negative and contains milliseconds, the file becomes the timestamp "Jan 1 1970", i.e. filetime is asumed as `0L`

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
    Calendar cal = Calendar.getInstance();
    cal.set(1960, 10-1, 12, 13, 25, 00);
    long millis = cal.getTimeInMillis();
    Files.setLastModifiedTime(file.toPath(), FileTime.fromMillis(millis));

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
The timestamp of the file should be "Oct 12 1960 13:25:00".
ACTUAL -
The timestamp of the file is "Jan 1 1970 00:00:00".

---------- BEGIN SOURCE ----------
import java.io.*;
import java.nio.file.*;
import java.nio.file.attribute.*;
import java.time.*;
import java.util.*;


public class FileTimesFromCalendar {

  static long getCalendarMillis(int year) {
    Calendar cal = Calendar.getInstance();
    cal.set(year, 10-1, 12, 13, 25, 00);
    return cal.getTimeInMillis();
  }
  static long getDateMillis(int year) {
    return switch (year) {
      case 1960 -> Date.parse("12 Oct 1960 13:25:00");
      case 1980 -> Date.parse("12 Oct 1980 13:25:00");
      default -> (new Date()).getTime();
    };
  }
  static long getInstantMillis(int year) {
    Instant instant = ZonedDateTime.of(year, 10, 12, 13, 25, 00, 0, ZoneId.of("CET")).toInstant();
    return instant.toEpochMilli();
  }
  static void touch(long millis) throws IOException {
    final File parent = new File("log/FileTimes"), file;
    parent.mkdirs();
    try (FileOutputStream out = new FileOutputStream(file = new File(parent, "FileTime"))) {
      out.close();
      Files.setLastModifiedTime(file.toPath(), FileTime.fromMillis(millis));
      System.out.println("Date of file: "+new Date(file.lastModified()));
    }
  }
  static void touch(Instant instant) throws IOException {
    final File parent = new File("log/FileTimes"), file;
    parent.mkdirs();
    try (FileOutputStream out = new FileOutputStream(file = new File(parent, "FileTime"))) {
      out.close();
      Files.setLastModifiedTime(file.toPath(), FileTime.from(instant));
      System.out.println("Date of file: "+new Date(file.lastModified()));
    }
  }

  public static void main(String[] args) throws IOException, InterruptedException {
    for (int i=0; i<3; i++) {
      System.out.println("Negative Millis ...");
      long millis = getDateMillis(1960);
      System.out.println("Millies from Date: "+millis);
      touch(millis);
      millis = getCalendarMillis(1960);
      System.out.println("Millies from Calendar: "+millis);
      touch(millis);
      long rmillis = millis / 1000 * 1000 - 1000;
      System.out.println("Millies from Cal rounded down: "+rmillis);
      touch(rmillis);
      rmillis = Math.floorDiv(millis, 1000) * 1000;
      System.out.println("Millies from floorDiv(Cal): "+rmillis);
      touch(rmillis);
      millis = getInstantMillis(1960);
      System.out.println("Millies from Instant: "+millis);
      touch(millis);
      Instant instant = Instant.ofEpochSecond(-290950500L, 12345678L);
      System.out.println("Millies from Instant with nanos: "+instant.toEpochMilli());
      touch(instant.toEpochMilli());
      System.out.println("touch from Instant directly: "+instant);
      touch(instant);
      System.out.println("Positive Millis ...");
      millis = getDateMillis(1980);
      System.out.println("Millies from Date: "+millis);
      touch(millis);
      millis = getCalendarMillis(1980);
      System.out.println("Millies from Calendar: "+millis);
      touch(millis);
      rmillis = millis / 1000 * 1000;
      System.out.println("Millies from Cal rounded down: "+rmillis);
      touch(rmillis);
      rmillis = Math.floorDiv(millis, 1000) * 1000;
      System.out.println("Millies from floorDiv(Cal): "+rmillis);
      touch(rmillis);
      millis = getInstantMillis(1980);
      System.out.println("Millies from Instant: "+millis);
      touch(rmillis);

      Thread.sleep(250);
      System.out.println();
    }
  }

}

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
// round down *absolutely* – for positive and negative values – to seconds with:
millis = Math.floorDiv(millis, 1000) * 1000;

FREQUENCY : always