I am currently running the L4 Epic Arcs, and didn’t have any issue with the Amarr one either.
In the Minmatar arc, however, so far I had 2 missions in Avesber and one in Jark, both of them EDENCOM Fortresses; and Eygfe, which became a Fortress too, is the access point to the Aptetter constellation, where the second chapter starts. Luckily, none of them became null and they all turned in the same direction, but it wouldn’t be doable were you friends with the Triglavians.
While I am yet to run the Gallente and Caldari arcs, at least the Hyasyoda path appears to be compromised for those of us aligned with EDENCOM in the latter: it would require flying to Wuos, and Inaya is a Triglavian Minor Victory.
This is what CCP Coyote had to say the other day on the matter:
Is there plans to remap the systems involved some the Epic Arcs missions post invasion? It’s just, that say Jark had gone Liminal rather than Fortress then completing the Sisters of Eve Epic Arc would be a lot harder.
I can’t speak to that, except to say that I imagine they’d be fixed if we broke them.