The program is trying to determine the amount of contributions you made to the Roth IRA you cashed out. You can withdraw contributions you made to your Roth IRA anytime, tax- and penalty-free. However, you may have to pay taxes and penalties on earnings in your Roth IRA. You aren't being asked about your other Traditional IRAs.
FYI, even though you couldn't roll your Roth IRA into one of your existing traditional IRAs, you could opened a new Roth IRA and rolled it over to that account. There are multiple financial institutions where you can open a no fee Roth IRA.
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