IRS Pub 590-A says:
Failure to report nondeductible contributions.
If you don’t report nondeductible contributions, all of the contributions to your traditional IRA will be treated like deductible contributions when withdrawn. All distributions from your IRA will be taxed unless you can show, with satisfactory evidence, that nondeductible contributions were made.
I would interpret that to mean that you must omit from line 1 of an amended Form 8606 for a particular year any amount for which you cannot provide evidence that you 1) made the traditional IRA contribution for that year and 2) that you did not deduct the contribution on your tax return for that year.
