After you file

The IRS seems to not know the cost basis for the UBS ones, so I need to update them on that. 

 

They seem not to know because that's how they do it ; they assume a basis of zero.

 

My question:  Do I send them a new Schedule D that includes BOTH UBS and Merrill, or do I send them a Schedule D that shows just the UBS transactions since the IRS already have my Merrill stuff from my original tax

return? 

 

There's only one Schedule D , I suggest including a correct and complete Schedule D.

That's what I suggested above.

Your missing transactions may end up in BOX A,D.

 

And should I send them a new Form 8949 that shows just the UBS transactions, or should it include both UBS

and Merrill? 

 

send a separate Form 8949 with details only for the missing transactions.

that's what I suggested above. that made sense if there was a box B,E subtotal for that amount.

You can send the entire set of 8949 documents if you prefer that.

 

Note: because of TurboTax new behavior for Box A and Box D, you might have difficulty.

and might  need to do the Form 8949 manually.

OR you can remind the IRS that Form 8949 is not required for Box A , D transactions without adjustments.

 

It depends on how many transactions are involved.

Once you supply the total cost basis, I suspect the IRS will be satisfied.

For best results, try to comply with the instructions in your letter.

Use your own judgement.