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Prevent JOption from blocking child JFrame

Is there a possibility to prevent a JOptionPane dialog from blocking the interaction with the rest of the program, especially child JFrames? In my GUI, I launch a JFrame and want a message dialog to pop up after the child is closed to remind the user of something, but they launch parallel and the reminder blocks the child frame from being used.
Like here:
popupObjMan newPopup1 = new popupObjMan(gatewayAbstract, gatewayAbstractID);
JOptionPane.showInternalMessageDialog(this, "REMINDER: DO REFRESH");
I've tried to set the popup always on top, but this doesn't quite do the job.
I have no problem with them launching parallel (I'd even prefer it), but I could not work my head around it yet.
I just started Java programming ,so sorry in case that'd be something obvious.

A JOptionPane normally need to be modal. It shows something important and waits till the user answers with whatever option you give him (e.g. ok-button, yes/no-buttons, ...)
But there are several ways to reach your target.
(a)
Normally a JOptionPane creates a modal window.
You need a modeless window which does not block other windows.
https://docs.oracle.com/javase/tutorial/uiswing/misc/modality.html
(b)
You can start different threads to work for your different windows. They can have windows which are shown whenever the responsible thread commands them to. This is a bit difficult and can lead to memory-troubles.
(c)
You can write your own message-panels (e.g. notificaton) which are shown when and how long you like.
Bigger projects use different of these ways to achieve their goals.

A JOptionPane is a component, just like a JPanel. As a component it can be added to any other panel.
The JOptionPane API provides static methods to create a show the JOptionPane on a modal JDialog by default. You can't change this behaviour.
However, you can manually add the JOptionPane to a non-modal JDialog that you create. This is extra work as you now need to handle the closing of the dialog and processing the clicked button.
If you really want to do this then read the JOptionPane API. There is a section on Direct Use which demonstrates the basic code needed to add the JOptionPane to a JDialog.

Close window - but don't stop program - JAVA

In my program it opens a window if an action is happened. After I have filled out information in this window, and entered a button, the window dispose().
The window is picked up in a program outside my main program, but when I close this window, my main program stops. How can I prevent this from happening?
Thanks for your help!

You can set the defalaultCloseOperation property of the second frame to DO_NOTHING_ON_CLOSE or DISPOSE_ON_CLOSE
Don't even use two frames. Use a modal JDialog instead for a secondary frame. See more at How to Use Dialogs. Read more about Modality. And for a good read, see The Use of Multiple JFrames, Good/Bad Practice?
Forget about number 1. and go straight to 2.

If using JFrame or extending it you can use setDefaultCloseOperation() method like:
frame.setDefaultCloseOperation(HIDE_ON_CLOSE);
// or
frame.setDefaultCloseOperation(DISPOSE_ON_CLOSE);

The dispose command is from the AWT Bundle, and this may cause problems, as you are attempting to "close" a swing window with an AWT command.
You can close the window with this command:
windowName.setVisable(false);
windowName is the name of the object representing the window. If you are extending a class, and have no object, you can use this
More Information on the Dispose Method:
"In general java.awt.Window.dispose() is used on a GUI component that is
a subclass of Window, in order for that specific GUI Window object (and
its children) to properly release and destroy native UI resources (such
as the screen). Garbage collection (and the eventual exiting of the
entire VM) may happen as a result of dispose(), but is not directly
connected with the dispose() call itself." From: https://www.java.net/node/684412

windowName.setVisable(false);
doesn't seems to be a good choice. What if user want to exit the program?
check this question - How to hide a JFrame in system tray of taskbar

Java Swing JFrame diposition

I have one JFrame. That JFrame has a window listener for closing events which are intercepted and provide the user with options prior to closing the entire program.
Must I call dipose() on a JFrame or am I safe to call only System.exit(0)? Secondly, should I only call dipose() on a JFrame or should I call dipose() followed by System.exit(0)?

My question is must I call dipose() on my JFrame object or can I safely call System.ext(0)?
Why would you ask this? You should solve you compile problem first, and then decide what approach you want to use. Don't use System.exit() just because you don't know how to get rid of a compile error
am using a WindowAdapter as
There is no need for you to keep a variable in order to reference your frame. The best approach to access the frame is to get the frame from the WindowEvent:
JFrame frame = (JFrame)event.getSource();
To answer your original question I would use dispose(). It will eventually invoke System.exit() if it is the last frame open in your application.
Edit:
I want to give the user an option to do something productive before closing the program down
You can check out Closing an Appliction for more ideas on this topic.

Why does my application terminate if user closes separate window?

I have a simple GUI program that creates a new window (which contains a JTable) at some point in time. If the user closes the JTable, the main application closes as well. How do I prevent this? Would it have something to do with how it handles the window closing, or should I give it it's own thread, or what?

Set one of these close operation for your JFrame: HIDE_ON_CLOSE or DISPOSE_ON_CLOSE.
You are using EXIT_ON_CLOSE.
Here is a link to the JavaDoc method you can use.

JDialog setVisible(false) vs dispose()

Does it make sense to use setVisible(false) on a dialog and reuse it later or is safer to call dispose() every time and to make a new JDialog.
What about memory leaks with setVisible(false)?
EDIT:
My Question isn't so much about quitting the application. More about Dialogs that have the main frame as parent and are opened and closed during the application life time. E.g. let's say my applications has about 10 dialogs that display different data every time I open them. Should I reuse the instances and use setVisible() or should I make a new Dialog every time and dispose() them on closing.

I would recommend using dispose() to release resources and free up memory. If you want to show the dialog again, simply invoke setVisible(true).
It's important to note that when the last displayable window within the Java virtual machine (VM) is disposed of, the VM may terminate. See AWT Threading Issues for more information.

I still can't see any diference between JDialog#dispose(); and JDialog.setVisible(false) more here, each of them could be wakeup for reuse, and doesn't matter if was/were Disposed or Visibled
my view is that this question must be splited to three separates areas
1) some JFrame is parent for JDialog or JWindow (exist only is is there JFrame), then last one must to turn-off the lights
2) without parent for JDialog
3) there still exist another JFrame, JDialog or JWindow, then last one must to turn-off the lights
reachable by using --> Window[] wins = Window.getWindows();
last one must to turn-off the lights --> System.exit(0);
I suggest that there in all of possible cases must exist visible JFrame with JFrame.EXIT_ON_CLOSE, or another way could be implements WindowsListener with System.exit(0);

Calling dispose() frees the resources associated with the dialog. You can keep the dialog around after you dispose() it. If you are worried about having too many dialogs laying around, use a WeakReference to hold the reference. That will ensure that your dialogs you are not using only survive garbage collection as long as the space they occupy is not needed.

I experienced a difference when a window shall be hiden twice (in cause of bad software design e.g.)
If you dispose an already disposed window the VM hangs. (java 8)
If you setvisible false on an already invisible window life goes on...