Yes, you can treat them as two separate transactions. The sale that is reflected on your W-2, can be entered as one transaction, and the sale of ESPP shares that were transferred out to another firm, and then eventually sold, can be treated as a separate transaction.
Based on what is happening, it appears that if you treat these transactions as two separate transactions, your return will be consistent with the information on your W-2 because that W-2 only reflects the sale of the ESPP shares that were held in the original account.
We do not know your offer dates, purchase dates or sell dates, so you will need to determine not only your gain or loss, but also what part of these transactions should be reported as compensation income. The compensation income, which gets taxed as ordinary income, should be on your W-2; however, the compensation income for the ESPP shares that you transferred to another firm, may not be reflected on your W-2. If it's not there, you still need to include it on your return as compensation income.
Here is a link to a TurboTax article that addresses ESPPs and taxes. This article provides examples of purchases/sales of ESPP shares and how to treat them for tax purposes.
Employee Stock Purchase Plans
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