Rolling over Traditional 401(k) affected by Pro Rata

I currently have three retirement accounts:

1. Account A: Traditional IRA with Pre-tax money
2. Account B: Traditional IRA with Post-tax money (used for backdoor Roth IRA)
3. Account C: Roth IRA
4. Account D: Traditional 401(k)

In the last 3 years, I have been doing backdoor Roth IRA from Account B to Account C. Unfortunately, I was not aware of the pro-rata rule and need to amend my returns to correctly reflect this.

Going forward, I want to continue doing backdoor Roth IRA and thinking of rolling over Account A into Account D so the balance in my Traditional IRA is zero. However, since I've "tainted" my traditional IRA balance due to the pro-rata rule, what happens when I roll over Account A into Account D?