At any point, you can go back in the pipeline and edit either the placement of your joints, or even your skeleton settings, adding or removing joints.
Furthermore, you can edit a character that has already been published through the Build Control Rig process.
If you are working on a scene, and need to edit a character using the Epic Games menu -> Edit Existing Character option, remember to save your scene. The character you choose to edit will force load into Maya to the determent of any progress made in the current scene.
SAVE YOUR WORK BEFORE CONTINUING
To edit a character that has been published, go to the Epic Games menu -> Animation Rigging Toolset -> Edit Existing Character:
This will bring up an interface for you to select a character to edit. The list is a list of all of the export files created by the tool:
Once you select a character and left-click Edit Export File, it will open the Character's export file and bring up the UI used for the rigging pipeline. Once loaded, you can make any changes you wish using the ART Rigging Toolset interface. Just make sure to re-build the control rig again if you have made any changes beyond skin weighting, once you are finished editing by using the Build Control Rig button.
Maya's referencing system is robust, you can make all the changes you want to and it will have a minimal impact on any work down the line (animation, skinning, etc...). This assumes no major changes are made to the naming and organization of the rig, otherwise changes will propagate up the reference chain.
An example of a major change would be if a character had a tail and you rebuilt the tail but with a new name, you would lose all animation and skinning data for those joints.
Other minor changes may still require the rework of animation.
Once the character is loaded, the ART Rigging Toolset will be in Deformation Setup mode, but you can cycle back to Skeleton Placement or Skeleton Creation and make any changes you want.
When entering Skeleton Placement mode from Skin Weight mode and you have a mesh skinned to the skeleton (the proxy geometry that is auto skinned does not count), you will get a prompt letting you know the tool will do its best to store skin data but it is not fool proof.
Joints added in Skeleton Creation mode will not automatically add themselves to the skinning data of the character mesh that was previously skinned to the skeleton. To add them just use the Add Influences button then select the new joints from the list.
New joints start locked and have no influence on the mesh.
Upon returning to Deformation Setup mode, saved skin data that was saved will be re-applied to the skinned mesh.