Yes, the IRS will have a copy of both W-2's. If they question your combined entry, it was done to report income distribution correctly in TurboTax for Box 11 (and be able to Efile). People do combined W-2 entries for issues similar to yours often.
If you only had one W-2 with a lesser amount in Box 1 than Box 11, then that's a problem for reporting properly in TurboTax.
The IRS usually figures out what was done.
@rsethi
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