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@dtamayo and I were looking into this during the workshop. This is what happens if you run the Migration notebook example in REBOUNDx with TRACE:

Part of what's happening here is at the point of disagreement, TRACE starts flagging the inner particle as undergoing pericenter approach. There's currently a bug in integrator.c where additional forces are not applied during pericenter flags. We can fix this issue by adding in a check for r->ri_trace.mode == 3
here.
Line 237 in 68944aa
Unfortunately, that's not the whole issue -- this makes things much better, but we still see disagreement.