Hi Whistler!
Well, I've found a solution, although I wouldn't called it 'elegant'.
The key is using different pilot profiles. I've created four pilot profiles, one for each era (I named them DOF-whatever, TGA-whatever, etc, to easily recognise them). In Users folder, I've copied the settings of my original profile to settings in all new profiles. Now I have a specific pilot to be used for each era.
I've also kept the default profile. Provided you are cautious enough to select only the corresponding profile to the active module, and you have activated the missions for this module via JSGME, changes in other modules won't affect your career.
For example, I've activated DOF campaigns with JSGME, opened IL-2 DOF module, selected my DOF profile, begun a DOF campaign.
Before shutting down, I've selected default profile. Now, I have deactivated DOF campaigns via JSGME, launched IL-2 DOF, selected default profile and gone to Pilot Career. Obviously, campaigns weren't there.
Now, shut down, activate again DOF campaigns in JSGME, launch IL-2 DOF, select my DOF profile, and 'voilà', there were my intact campaign!
I hope you can understand this convoluted explanation. The secret is having one profile for each era, and be careful not to select the wrong pilot in the wrong module. Default pilot can be used as a firewall, and to see what campaigns are activated or not without spoiling your progress.
Cheers!