I mistakenly thought your amended returns used the corrected numbers.  I'm sorry about that misunderstanding.

Ideally, transfer a file that has the ACTUAL numbers that the IRS finally ended up with.

However, in most cases, it won't matter.  It really only would affect if the changed AGI affected any carryover numbers. 

As far as your comment about the most recent AGI for security check, are you using ProSeries?  I don't think the prior-year AGI method is even an option for tax professionals, is it?