Do I report an undetermined term transaction for noncovered tax lots on a 1099-B form?

Yes, because otherwise you will receive a letter from the IRS called a CP2000, along with a bill based on the gross amount of these transactions.  

You will enter unknown term gains or losses in the 1099-B interview along with your other stock transactions, but you will need to provide the missing purchase date or manually choose long-term or short term transaction.  When it comes to the date acquired, your 1099-B can still be useful (even though it left this area blank). As long as each sale was listed as either short-term or long-term, you can type in the word "Various" in the box for date acquired.

When you enter or edit the specific transaction and do not include a purchase date, you will see the page Tell us about your no purchase date 1099-B.  Your 1099-B likely reports this as a Box X transaction, so select that option next to Sale Category.

This will open another menu where you can choose the long-term (over a year) or short-term (less than a year) option.  If you don't know how long you've had it, the transaction is automatically considered short-term.