Ew, no. Keep SCH and PCB in sync. To do otherwise is madness. Sooner or later you'll forget what you did, and things get screwed up...
One way you could do this is to put everything that *doesn't* change into separate schematic(s), and the one thing that does change, into a separate schematic (one for each version). Start two projects, each with all the common schematics, and one with the first schematic variant, and the other with the other. Now you have two PCB projects, which means all the schematics that generate the PCB, and the PCB, and the project settings for them. By using common schematics, you avoid the madness of having to sync two PCBs.
By far the best is to use a single project, one common footprint (assuming they don't conflict), or two footprints (in different locations, again to avoid conflict). If neither of these is possible, and you really need two separate PCBs, then you're better off using two separate PCBs.
It's noteworthy that variants can be selected in the OutJob for fabrication outputs too, but I don't know if that's useful here or not. If so, it again seems like a good way to generate confusing outputs (are these files, in the same folder and with the same file names, from variant A or B?).
Tim