I am always amazed that taxpayers don't notice extra withholding for the wrong state/locality had been deducted from their pay through the year until when it comes time to file their returns.  Your client should, hopefully, have approached the employer by now to fix it for 2023.

Under Income > Wages, Salaries, Tips (W-2), on the W-2 tab, scroll down to the New York section, and enter -1 (which stands for 0, PTO/Lacerte-speak) on the line for Wages subject to Y-203 (1=all).

This way, Y-203 won't be prepared but Yonkers LIT will still flow through to IT-201, line 74.

If your client gets a notice for Yonkers nonresident tax, a W-2C may then need to be issued but you can probably cross the bridge when you come to it.