It is not clear just what the IRS "notified" you about. They usually only notify you of errors on your tax return.
To answer your question:
1) There is no such thing as a "non-deductible" IRA. A Traditional IRA can contain non-deductible contributions which become a basis in your IRA.
2) You only have one Traditional IRA which is the aggregate total of ALL Traditional IRA accounts that you might have.
3) The non-deductible "basis" applies to ALL such Traditional, SEP and SIMPLE IRA accounts that you might have.
4) You can NEVER withdraw or convert ONLY the nondeductible part - it must be prorated over the entire value of ALL Traditional IRA accounts which include SEP and SIMPLE IRA's. (For tax purposes you only have ONE Traditional IRA which can be split between as many different accounts as you want, but for tax purposes they are all added together).
For example using rough figures: if you had $60K of nondeductible contributions in an IRA with a total value of $600K (10:1 ratio), then when you take a $60K distribution from any IRA account $6,000 would be nontaxable and $54,000 would be taxable (same 10:1 ratio) , with the remaining $54K of basis staying in the IRA for future distributions. As long as there is any money in the IRA, there will be some basis.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
