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Hey Hanno, this one was quite tricky but think I figured it out!
Some issues with the scope of nbody_ode. After a merge (and seemingly only after a merge), only the local variable nbody_ode is updated, not the global r->odes[0]. To be honest I don't entirely understand why your code didn't work, everything looked fine to me - but I reassign y within the loop now and it seems to work.
Unrelated bug, but realized over the course of debugging that it's important to still update the actual r->t variable during the bs step. collision_resolve checks the last time of collision against the current simulation time, so this fails if the collision happens during the first call of bs_step.