We amended our LLC tax returns for 2011 and 2012 voluntarily.
IRS didn't issue any notice and we amended voluntarily on the basis of another CPA's review. The main issue with the original LLC return was that our original CPA deducted expenses instead of capitalizing them. The 2nd CPA wanted to be more conservative and not deduct any expenses, which we agreed. Ours is a start up (construction phase) and we haven't opened business yet.

Would IRS review/audit the original returns that were audited?
Since our LLC is based on partnership, there were no tax implications.

A small typo in my original thread

Would IRS review/audit the original returns that were audited?

Should read

Would IRS review/audit the original returns that were amended?

Filing an amended return does not affect the selection process of the original return. However, amended returns also go through a screening process and the amended return may be selected for audit. Filing an amended tax return does not, in and of itself, "red flag" you for an audit. However, the IRS notes that amended returns go through a screening process just like regular returns, which could result in an audit. So, filing an amended return adds an extra layer of IRS scrutiny of your taxes. If you do file an amended return, you can reduce your audit risk by attaching copies of supporting documentation. Providing evidence upfront minimizes the chances of the IRS looking at your return any longer than it has to. SO, basically, filing an amended tax return does not, in and of itself, "red flag" you for an audit; amending a return may increase the audit risk, but probably not as much as you think. It really depends on the items included or excluded in the amended return.

Thanks for the detailed update.
My question was regarding the review of the original returns. I am not concerned about the audit/review of the amended returns since our CPA took a very conservative approach. But the original returns prepared by a different CPA was more aggressive. Can we assume that IRS will always review the latest amended return and not the original return since the original return anyway has errors (which is why it was amended)? Even if IRS audited original return and found errors which were already fixed in our amended return, what action can they take?

Correct.As far as I know, filing an amended return does NOT affect the selection process of the original return. However, as mentioned previously, amended returns also go through a screening process and the amended return may be selected for audit. Amending a return may increase the audit risk, but probably not as much as you think. It really depends on the items included or excluded in the amended return.