One difference between oil based and water based is that oil based usually gives an orange tint to the wood. Water based is usually clear, so the finish comes out different between the two.
You can get the oil based look by using a dewaxed shellac on the wood as a sanding sealer before you apply the water based finish. The shellac gives the orange color to the wood.
To answer you actual question, you should be able to apply oil based over water based but sand the water based finish to give the oil based something to grab on to.
Unless the table is really large (or the finish really thick), I'd sand it down and re-finish.
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