If you have a reasonable size connector attached to a custom component there are two ways you can quickly rename the Connector ID.
Right click on the custom component and use the assign connector, using the new Connector ID. The only problem with this is that all of the pins of the component will be assigned the Connector ID, it will also only be limited to changing the Connector ID on the component you are working on - not good if it's and Electronic Control Unit that you have split across several pages.
If you edit one of the pins of a component and change the Connector ID's VeSys assumes you are trying to assign the pin to a different connector. Let's say you have a Connector ID J001 and you need it to be renamed P104 the following steps will enable you to do this:
Edit one of the Pins of Connector J001
Assign a temporary Conenctor ID to the opposite half (either male or female) i.e. 'Fred' and then click OK
You will now have a connector 'J001' and 'Fred', go back into the Connector and rename 'J001' to 'P104' and again click OK
Go back into the Connector again and remove the Connector ID 'Fred' and click OK
Note: You will have to keep exiting the dialog in order for this to work you cannot shorten it or VeSys will assume you are linking the Pin to a new set of Connectors.