As long as you entered the correct "cost or other basis" when you reported these sales, it doesn't matter whether you identified the shares as coming from an ESPP or not - there is no need to amend any returns where the sales were reported.
Once your spouse left the company and transferred the stocks into a regular brokerage account, they are just treated as regular stock holdings. Since they were purchased at a discount through an ESPP, it is your responsibility to keep track of the actual cost.
