Do you have a sample source code where this happens?
From the symptoms it would seem as a race condition somewhere but can't tell for sure till I have something to debug the problem :(

The code was like bellow:
---------------------------------------------
import javafx.scene.CustomNode;
import javafx.scene.Group;
import javafx.scene.Node;
import javafx.scene.paint.Color;
import javafx.scene.shape.Rectangle;
import javafx.scene.text.Text;
import javafx.scene.text.Font;

class MyNode extends CustomNode {

    public override function create(): Node {
        Group {
            content: [
                Rectangle{
                    fill: Color.GREEN
                }
                Text{
                    font: Font{ size: 20 }
                }
            ]
        }
    }
}
---------------------------------------------


Where I changed the 'Group' to 'Stack' in the create() function 
and invoked Fix Imports.

I am not able to reproduce it :( Next time you see this problem could you attach the IDE messages.log file as well? I might be able to get some indices from those (hopefully). 
Till then I would lower the priority to P3 since the issue is highly random with the tendency not to happen.

Steps to reproduce.

 - Check that the issue 184799 is not fixed

- Create a JavaFX file
- Create aaa.bbb pakage
- Create A class under the package
---------------  A.fx -----------------
package aaa.bbb;

public class A {}

public class B{}
-----------------------------------

- Copy the code to the Main file
-----------------------------------
package javafxapplication1;

var a= A{};
var b = B{};
-----------------------------------

- Invoke Fix Imports several times

The line 'import aaa.bbb.A.B;' is added, removed, added, removed and then broken:

-----------------------------------
package javafxapplication1;
i
import aaa.bbb.A.B;mport aaa.bbb.A;

var a= A{};
var b = B{};
-----------------------------------

Created attachment 97906 [details]
IDE log file

hopefuly fixed by http://hg.netbeans.org/javafx/rev/2a7beebf951d

unable to reproduce in build netbeans-trunk-nightly-201005170932-javafx-windows.exe