One way to reposition the gingival would be to start a new job and take another scan of the model with the gingiva in the right position on the model. Import this model as generic visualization mesh(or other mesh type you aren't currently using) and register it to the jaw scan. Once you have that new scan in the proper position use add/remove mesh, select gingiva, click register mesh and match to the new scanned models position. Gingiva is now in proper position, you can use expert mode to free form the basal and other areas, next use adapt pontic to gingiva and click ok to save your changes.
Changing the bite position during design can be done using add/remove mesh and select antagonist. You will have the option to change the positioning by vertical (z axis),horizontal (x,y axis) or move freely. IMO this is fine for minor tweaks, but is similar to having two models with a wonky bite that don't interdigitate very well. Your just guessing.
There is a way to import a new bite scan and reregister the positioning, but I am not in front of a machine today to lay out verified steps.
There is also an xml file edit to add another option to reposition jaw relationship during design. It is considered a prototype at this time and may be made a regular option on the next release, but again I'm not near a exo machine today to provide the added node for the xml or verify the steps, sorry.
