Seems like one way to keep things reasonably in sync is to define a base exposure time and then require exposures to be an integer multiple of it.  E.g. you might chose a base of 120 seconds and one train could be taking 1x (120 s) subs while the second is doing 3x (360 s) subs.  Given some slop for file transfer things would more or less be in sync so dithering for example could take place when you have a break in both - by definition it would be dithering on only the longer subs timebase.  This would allow some flexibility to account for differences in filter/aperture/saturation.  Same would apply for refocusing with attendant pause in guiding for OAG, you wait for all trains to be complete and then focus everyone.  Due to the fact things would be a little offset due to breaks between shorter subs you would loose a little efficiency compared to each train running its own sequence totally independently.  It would be more flexible than requiring all trains to image at same exposure time and has less chance of error than relying on operator to construct sequences where the subs are integer multiples of one another.

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