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When the time comes to take money out of IRAs, you will be asked to state the total which represents non-deductible contributions, and for the purpose of calculating tax to be paid on the distribution, the accounts are to be regarded as all one.
If you have rollover and contributory IRAs, there is a possible benefit in keeping them separate on the off chance that someday you might like to roll a former employer's 401k money into a new employer's 401k plan. If you have intermixed the moneys, you lose that option.
With deductible and non-deductible IRAs, I can't think of any reason to keep them separate since the law treats them as mixed in any case.
Best wishes, Chris
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