The fact that the delete option for a nail and a transition shares the same name in the popup menues can cause the user to mistakenly think that he/she has deleted a transition when actually he/she has only deleted a nail in the transition. This can occur when two transitions go from state A to state B and the one (C) is direct and the other (D) has exactly one nail. If the D transition has no Guard, Sync. or Update (yet) and the nail is deleted this transition (D) will seem to disappear, but actually it will just coincide with the C transition.
Parhaps the names in the popup functions should be "delete transition" and "delete nail".
In fact, I think UPPAAL should refuse to delete the last nail. If I remember correctly, you cannot create such invisible transition in the first place, so you should not be able to "downgrade" a loop with one nail to a loop without any nails.
Changed the label on the delete menu item. I leave this bug open, since I feel there is a bigger issue with having multible transitions between the same two locations (as descriped by the reporter), but there is no time to fix this for 3.4.
Moved enhancement request to 3.5.7, as only bug fixes are allowed in previous releases.
I changed it such that deleting the last nail of a self loop also deletes the edge.