Is there a library part associated with the connector?
No, it also occurs when adding a `fresh' connector, with the button in the toolbar.
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OK, I asked because obviously if a library part is associated it should never create a pin that does not exist on the part in the library.
The automatic pin-numbering in VeSys works on a "high-watermark" basis (per connector). This means that even if some pins are deleted, the numbering always continues from the highest ever pin number for that connector. This is important in some markets where they are not allowed to re-use pin names (even if they are deleted). It may be possible to reset the counter, but I do not believe that is possible in VeSys (Advanced Naming in CHS does support it).
When I add a library part, the pin numbering is automatically resetted.