An IRA custodian has no way to know your basis. It's your responsibility to track that and make sure that on the date of the distribution being rolled over from the traditional IRA to the 401(k) that the amount being rolled is less than or equal to the value of your traditional IRAs minus your basis in nondeductible traditional IRA contributions. (Given recent market volatility, you might want to consider rolling over a bit less than your pre-tax amount and accept a bit of your Roth conversion being taxable when you convert all remaining traditional IRA funds to Roth.)
