Any money that you withdraw from a Roth IRA will be not be taxed unless it is an early distribution. In that case, only the earnings withdrawn would be taxable. So, if you had the Roth IRA for five years before you took the distribution and you were over 59 1/2 years old when you took the distribution, none of it would be taxable.
Furthermore, from what you said there were not earnings in the account, so there would be no tax for that reason as well.
No one can know if the IRS will inquire about the entries, but if you keep documentation supporting what you explained here you should be OK.
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