You will need to adjust that amount on the 1099-R and not by trying to change the number on the form.
Go back to where you entered the 1099-R into the system and adjust the taxable amount in box 2a to reflect what you think it should be (in your case sounds like zero). Then file the return. Keep all of the records that prove that this was not a taxable distribution so that you can show them to anyone down the road if it is requested.
@1jmotheral
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