ADDITIONAL SYSTEM INFORMATION :
OpenJFX 13, 14, 15 and 17.

openjdk version "11.0.12" 2021-07-20
OpenJDK Runtime Environment (build 11.0.12+7-post-Debian-2)
OpenJDK 64-Bit Server VM (build 11.0.12+7-post-Debian-2, mixed mode, sharing)

Linux 5.10.0-8-amd64


A DESCRIPTION OF THE PROBLEM :
I am not the original author of the bug report but I created a minimal reproduction example since I am also experiencing this bug.

It happens when the the observable list that a sorted list is based upon is changed a second time as a result of the original change.
Important: This is also a problem if the original list is already empty when calling the second "clear()" it will remove the items a second time for some reason.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run the code example as junit test (test-fx)

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Passes without exception – at the clear step to be precise.
ACTUAL -
Exception:

value handler start
value end
clearing list
value handler start
value null, clearing source list: []
--- Exception in Async Thread ---
java.lang.ArrayIndexOutOfBoundsException: arraycopy: length -6 is negative
java.base/java.lang.System.arraycopy(Native Method)
javafx.collections.transformation.SortedList.removeFromMapping(SortedList.java:364)
javafx.collections.transformation.SortedList.addRemove(SortedList.java:398)
javafx.collections.transformation.SortedList.sourceChanged(SortedList.java:108)
javafx.collections.transformation.TransformationList.lambda$getListener$0(TransformationList.java:106)
javafx.collections.WeakListChangeListener.onChanged(WeakListChangeListener.java:88)
com.sun.javafx.collections.ListListenerHelper$SingleChange.fireValueChangedEvent(ListListenerHelper.java:164)
com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:73)
javafx.collections.ObservableListBase.fireChange(ObservableListBase.java:239)
javafx.collections.ListChangeBuilder.commit(ListChangeBuilder.java:482)
javafx.collections.ListChangeBuilder.endChange(ListChangeBuilder.java:541)
javafx.collections.ObservableListBase.endChange(ObservableListBase.java:211)
com.sun.javafx.collections.ObservableListWrapper.clear(ObservableListWrapper.java:157)
de.gsi.bpeter.experiments.fxplain.sortedlistbug.SortedListBugTest.lambda$2(SortedListBugTest.java:49)
com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:360)
com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:106)
javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:113)
javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:147)
javafx.scene.control.ComboBoxBase.setValue(ComboBoxBase.java:151)
javafx.scene.control.ComboBox.updateValue(ComboBox.java:516)
javafx.scene.control.ComboBox$3.changed(ComboBox.java:499)
com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:360)
com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
javafx.beans.property.ReadOnlyObjectPropertyBase.fireValueChangedEvent(ReadOnlyObjectPropertyBase.java:80)
javafx.beans.property.ReadOnlyObjectWrapper.fireValueChangedEvent(ReadOnlyObjectWrapper.java:102)
javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:113)
javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:147)
javafx.scene.control.SelectionModel.setSelectedItem(SelectionModel.java:105)
javafx.scene.control.ComboBox$ComboBoxSelectionModel.lambda$new$0(ComboBox.java:556)
com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:136)
com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
javafx.beans.property.ReadOnlyIntegerPropertyBase.fireValueChangedEvent(ReadOnlyIntegerPropertyBase.java:78)
javafx.beans.property.ReadOnlyIntegerWrapper.fireValueChangedEvent(ReadOnlyIntegerWrapper.java:102)
javafx.beans.property.IntegerPropertyBase.markInvalid(IntegerPropertyBase.java:114)
javafx.beans.property.IntegerPropertyBase.set(IntegerPropertyBase.java:148)
javafx.scene.control.SelectionModel.setSelectedIndex(SelectionModel.java:69)
javafx.scene.control.ComboBox$ComboBoxSelectionModel$2.onChanged(ComboBox.java:587)
javafx.collections.WeakListChangeListener.onChanged(WeakListChangeListener.java:88)
com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(ListListenerHelper.java:329)
com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:73)
javafx.collections.ObservableListBase.fireChange(ObservableListBase.java:239)
javafx.collections.ListChangeBuilder.commit(ListChangeBuilder.java:482)
javafx.collections.ListChangeBuilder.endChange(ListChangeBuilder.java:541)
javafx.collections.ObservableListBase.endChange(ObservableListBase.java:211)
javafx.collections.transformation.SortedList.sourceChanged(SortedList.java:111)
javafx.collections.transformation.TransformationList.lambda$getListener$0(TransformationList.java:106)
javafx.collections.WeakListChangeListener.onChanged(WeakListChangeListener.java:88)
com.sun.javafx.collections.ListListenerHelper$SingleChange.fireValueChangedEvent(ListListenerHelper.java:164)
com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:73)
javafx.collections.ObservableListBase.fireChange(ObservableListBase.java:239)
javafx.collections.ListChangeBuilder.commit(ListChangeBuilder.java:482)
javafx.collections.ListChangeBuilder.endChange(ListChangeBuilder.java:541)
javafx.collections.ObservableListBase.endChange(ObservableListBase.java:211)
com.sun.javafx.collections.ObservableListWrapper.clear(ObservableListWrapper.java:157)
de.gsi.bpeter.experiments.fxplain.sortedlistbug.SortedListBugTest.lambda$5(SortedListBugTest.java:69)
java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:457)
java.base/java.security.AccessController.doPrivileged(Native Method)
com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:456)
com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(GtkApplication.java:290)
java.base/java.lang.Thread.run(Thread.java:829)


---------- BEGIN SOURCE ----------
package de.gsi.bpeter.experiments.fxplain.sortedlistbug;

import org.hamcrest.Matchers;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.testfx.api.FxAssert;
import org.testfx.api.FxRobot;
import org.testfx.framework.junit5.ApplicationExtension;
import org.testfx.framework.junit5.Start;
import org.testfx.matcher.base.NodeMatchers;

import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.collections.transformation.SortedList;
import javafx.scene.Scene;
import javafx.scene.control.ComboBox;
import javafx.scene.layout.StackPane;
import javafx.stage.Stage;

/*
 * Minimal bug example intended for:
 *
 * https://bugs.openjdk.java.net/browse/JDK-8162592
 */
@ExtendWith(ApplicationExtension.class)
class SortedListBugTest {

    private ComboBox<Integer> comboBox;

    @Start
    private void start(Stage stage) {
        comboBox = new ComboBox<>();
        stage.setScene(new Scene(new StackPane(comboBox), 100, 100));
        stage.show();
    }

    @Test
    void testThatListIsSorted(FxRobot robot) {
        ObservableList<Integer> observableList = FXCollections.observableArrayList();
        SortedList<Integer> sortedList = new SortedList<>(observableList, Integer::compare);

        robot.interact(() -> {
            comboBox.valueProperty().addListener((obs, old, value) -> {
                System.out.println("value handler start");
                if (value == null) {
                    System.out.println("value null, clearing source list: " + observableList.toString());
                    // list is empty so actually nothing should happen
                    // bpeter: Test works without the following line
                    observableList.clear();
                }
                System.out.println("value end");
            });

            comboBox.setItems(sortedList);
        });

        robot.interact(() -> {
            observableList.setAll(10, 9, 20, -5, 100, -3, 0, 4);
        });

        robot.interact(() -> {
            comboBox.getSelectionModel().select((Integer) 20);
        });

        FxAssert.verifyThat(robot.from(comboBox), NodeMatchers.hasChild("20"));

        robot.interact(() -> {
            System.out.println("clearing list");
            observableList.clear();
            System.out.println("clearing list done");
        });

        FxAssert.verifyThat(robot.from(comboBox), Matchers.not(NodeMatchers.hasChild("20")));
    }
}

/**
 * Dependencies
 *
 * <pre>
        <dependency>
            <groupId>org.junit.jupiter</groupId>
            <artifactId>junit-jupiter-api</artifactId>
            <version>5.5.1</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.hamcrest</groupId>
            <artifactId>hamcrest-core</artifactId>
            <version>2.2</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.testfx</groupId>
            <artifactId>testfx-junit5</artifactId>
            <version>4.0.16-alpha</version>
            <scope>test</scope>
        </dependency>
 * </pre>
 */

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

CUSTOMER SUBMITTED WORKAROUND :
Try not to change the original list maybe, but might be hard for larger constructs.