Did I ruin my save?

I ended up skipping the Forest Layer by speeding through the Freezer layer and just jumping the gap in The Junction over to where you'd come from for Forest Layer. I've gone back later and unlocked the sinkhole in Forest, but there was no boss that activated. I broke the Void Arrow surrounded by the thorns and Abracajabya did not appear. Did I miss something, or did me skipping the layer and going back after beating The Junction remove my ability to fight it?