So I'm also trying to understand what the issue is. You don't want people to backtrack, I get it. So don't backtrack.
Have they fought the BBEG yet? Did you leave them on a cliff-hanger where they knew the next fight was going to be the BBEG? No? Then there's still time to run into the mini-boss before they do. The mini-boss is in the next room they enter. Mods aren't set in stone and there have been several suggestions on how to insert the missed piece.
Or just change the mod. They really only needed 2 rods. Who knew! Or they needed 2 rods plus some other sacrifice/encounter/quest to complete their goal.
What's stopping you from running the "missed" piece as the next set of encounters before they hit the BBEG?
