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No idea why you could not just drill over the old holes. People do that all the time.
You may want to check out a how to video Melevsreef posted recently.
Only difference I see in your case is you would need to plug the existing holes temporarily to keep the water pooled while are drilling the larger hole over top.
Plumber's putty may be enough to plug as you just need it to pool water to keep the bit cool and flush cuttings.
+1 very good advice.Drain tank. Flip on side. Use guide and a garden hose. I've done many times.