Temporarily answering myself, but waiting for a better solution:
As a workaround I did several try.
The only one that seems work is to reload the main css file "modena.css"
It can be found inside the jar file under
"C:\Program Files\Java\jre1.8.0_131\lib\ext\jfxrt.jar
or under
C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\jfxrt.jar.
At least on my pc and in the above java version.
Open it with a decompressor (RAR, ZIP, ...) and under
"com\sun\javafx\scene\control\skin\modena\"
there is the file "modena.css". Copy it in the "Files" folder under the Application folder.
Now load it with the B4J ide in the files tab.
In the Application use the code:
Dim jo As JavaObject = MainForm.RootPane
jo.RunMethodJO("getScene",Null).RunMethodJO("getStylesheets",Null) _
.RunMethod("add",Array(File.GetUri(File.DirAssets, "modena.css")))
or
Dim jo As JavaObject = MainForm
jo.GetFieldJO("scene").RunMethodJO("getStylesheets",Null) _
.RunMethod("add",Array(File.GetUri(File.DirAssets, "modena.css")))