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@SEtaxpros wrote:

...So ultimately she will have a CT liability on those telecommuting days.

In Lacerte - I will need to subtract all income related to NY workdays as an adjustment to the Federal AGI leaving in her CT telecommuting days.  

The NY return will have the whole income amount with no wage allocation to CT.

Any idea why the NY withholding will not be pulling through to the State return?...

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Your first statement above is correct.  But what are you trying to do with the following two statements?  And what NY tax are you trying to pull through to the CT return and for what purpose?

If your client had actual NY workdays, I can see a credit being claimed on the CT return for those particular days but you will need to manually override NY source income subject to CT tax and the related NY tax liability on the input screen for other state tax because Lacerte will otherwise consider the full amount to be eligible for credit.