I don't understand the concern.
First, she contributed money to a tradition pre-tax IRA.
Next, instead of leaving the money as cash, she bought some investments, still in the IRA.
Is that it?
That's no problem at all. Just sell the investments and do a rollover to the Roth IRA. What you do with money inside an IRA is largely irrelevant. The backdoor Roth conversion can still happen whether the IRA balance is in a cash account or investments, it's just that the IRA trustee will have to sell the investments when you perform the rollover.
Now understand, for a "back door Roth conversion" to work, a person has to rollover/convert their entire balance in traditional IRAs. If your wife has two IRA accounts each with funds, she has to rollover both accounts, and if part of the balance is a pre-tax (deductible) contribution, there will be some tax on the conversion. But moving money from a cash account to an investment within the IRA does not create a separate IRA.
