So for example, after MECO/dump you could set up everything for the OMS-2 burn, fix the sunset TIG and correct Ti DVZ, and then save these changes as a FDO config under a new name. You could then theoretically use the newly named config, by deleting maneuvers and recalculating as usual along the way as you progress through the burns, all the way to docking, without saving again. This way of "no sequential FDO config saving" other than the initial OMS-2/SS/Ti save would work for a single sim session, launch to docking. A single start to finish session is typically how I use orbiter; I rarely save and re-visit any mission.
Alternatively, if you want to save the FDO configs each time as you progress through the burns, you'd have to save a concomitant scenario as well, so that you could restart the scenario, and have the associated renamed FDO config available to load and match the saved state of the SSV?
Am I understanding this correctly?