This will register a duplicate livery each time it is saved.
https://github.com/jamespetts/simutrans-extended/blame/ex-15/dataobj/livery_scheme.cc#L78
You can see that deleting this line eliminates duplicate registrations.
However, the livery scheme code has many different changes from the master branch, so I am not sure of the intent.
I believe that this was fixed a short while ago.