I have now reproduced a drag-and-drop issue with the TLC Merchantile BIQ. Steps (for my future self as much as anything):
This was due to not updating the (Swing) unit list in this case. Which might seem unnecessary... but the reordering code updates both. And even if it weren't for that, the stealth targets/legal unit telepad lists were not updated properly.
This is another data point in favor of separating the JavaFX and Swing code completely. The complexity of the Unit Tab still counters that for now, however.
Also note that the D&D part of the bug only happened when you attempted to reorder the last unit, which had been added after scenario start. The telepad/stealth parts would happen regardless of reordering it, however.
Fixed.