The VA situation is going to be...interesting in the next few years, since:The methodology for *cost* assignment was settled by the STB ruling, *including* the split for through trains IIRC.And, to elaborate on the allocation of costs and revenue of through trains between HAR and NYO, the methodologies used to assign costs and revenue will be a huge issue for PennDOT in it's negotiations with Amtrak.
(Although the "capital charge" still hasn't been developed.)
The methodology for *revenue* assignment seems to be less settled; I think the STB ruling contains a methodology but it's still kind of vague. More significantly, it only applies to trains which have a "net cost" -- Virginia has the question of how to split Lynchburg profit, though I believe the deal is that that will first offset Virginia's costs for other trains, and then go into a sequestered fund for capital improvements within Virginia.
1) Some revenue is going to be "lost" to the formula rework.
2) NS is demanding a higher fee going forward for the Lynchburger (I think that goes up by $1.5m in a year or two).
3) On the other hand, the WAS-RVR-NPN route is doing far better this year than in previous years, and I recall overhearing that as of some point, the majority of those trains actually turn a profit as well (it's either 3 of 5 or 4 of 5)...but the route loses money because of the relative margins. What's more, the situation has also been improving dramatically, so it might only be one of them that loses money...and apparently that's also expected to change once the Norfolk train gets going.
So VA might get into a situation where the two routes reverse position...which would give everyone involved headaches.
I suspect that you're right about there being a sequestered fund, either for capital improvements or against seasonal losses/disruption-heavy seasons (looking at the latest monthly reports, there are some trains posting seasonal profits but full-year losses, so it seems possible that some of VA's trains might make money for part of the year but lose money narrowly at the slowest times of the year). Still, if PPR can outpace costs and ridership can keep growing (which seems likely in the long term, considering how bad the various interstates are getting), this could be an interesting situation going forward.