ADDITIONAL SYSTEM INFORMATION :
reproduces on:
OpenJDK Runtime Environment (build 1.8.0_252-b09)/Linux x86_64
OpenJDK Runtime Environment (AdoptOpenJDK)(build 1.8.0_252-b09)/Linux x86_64
Java(TM) SE Runtime Environment (build 1.8.0_251-b08)/Linux x86_64

does not reproduce on:
OpenJDK Runtime Environment (AdoptOpenJDK)(build 1.8.0_232-b09)/Linux x86_64

A DESCRIPTION OF THE PROBLEM :
It seems that changes introduced in JDK-8232003 lead to two successive calls of com.sun.nio.zipfs.ZipFileSystem.EntryOutputStream#close() method which in turn leads to creation of empty zip file entries.

REGRESSION : Last worked in version 8

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
~]$ javac ZipFilesWrite.java
~]$ java -ea -cp . ZipFilesWrite
~]$ echo $?
0


ACTUAL -
 ~]$ java -ea -cp . ZipFilesWrite
Exception in thread "main" java.lang.AssertionError
at ZipFilesWrite.main(ZipFilesWrite.java:28)
~]$ echo $?
1

---------- BEGIN SOURCE ----------
import java.io.FileOutputStream;
import java.net.URI;
import java.nio.file.*;
import java.util.Collections;
import java.util.HashMap;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
import java.util.zip.ZipOutputStream;

public class ZipFilesWrite {

    public static void main(String[] args) throws Exception {
        Path zip = null;
        try {
            zip = Files.createTempFile("8232003", ".zip");
            try (ZipOutputStream out = new ZipOutputStream(new FileOutputStream(zip.toFile()))) {

            }
            URI uri = URI.create("jar:file:" + zip.toUri().getPath().replace(" ", "%20"));
            try (FileSystem fileSystem = FileSystems.newFileSystem(uri, new HashMap<>())) {
                Path root = fileSystem.getRootDirectories().iterator().next();
                Path manifest = root.resolve("test.txt");
                Files.write(manifest, Collections.singletonList("Main-Class: " + ZipFilesWrite.class), StandardOpenOption.WRITE,
                        StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.CREATE);
            }
            ZipFile zipFile = new ZipFile(zip.toFile());
            ZipEntry zipEntry = zipFile.getEntry("test.txt");
            assert zipEntry.getSize() > 0;
        } finally {
            if (zip != null) {
                Files.deleteIfExists(zip);
            }
        }
    }
    
}

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

FREQUENCY : always