Have you run this scenario through a future form 8606 (lines 1-14) yet?
At first I thought that you would have problems when you tried to do this, but I mocked up a simple example that was designed to capture the essence of your situation. The result was that the non-taxable basis in the IRA is preserved even though funds were rolled over into the Traditional 401k.
When, in the future, you rollover from trad 401k to trad IRA, the 401k people will report that 100% of the distribution is taxable (assuming that they do not change how they are accounting for your deposit). Then you would have the money (and the non-taxable basis) back in the IRA.
I don't 100% trust this argument yet, however, for the following reason. Let's say that the 401k properly coded your in-bound rollover as after-tax money. Then when the money is distributed back, it would be reported as after tax. You could just keep the money and not pay tax on it & still have the after-tax basis still in the IRA. You have effectively doubled the amount of your tax-free dollars -- basically a tax arbitrage!
Obviously there is a fallacy in here somewhere. I believe that I am probably missing something. Perhaps 401k plans are prohibited from accepting after-tax rollovers from IRAs. Would need to research that further. If traditional 401ks are indeed prohibited from accepting after-tax IRA rollovers, then my logic may hold up and you might not have a problem.
-gauss