Hi georgieh,
You do have a couple of options here. Yes, you can reverse those affected pay runs and re-process correctly. Because this category is an Employer Contribution, it should not have affected your net pay. Meaning your reconciliation should stay unaffected.
Alternatively, you can put an adjustment pay run through with the same dates, and put a positive figure against that-category-ONLY (offsetting the negative), then it should allow you to clear it through Pay Liabilities/ Pay Superannuation.
Let me know if you would like further assistance with these and I can show a step-by-step in doing an adjustment pay.