Can my employer deduct vacation pay from my last paycheck after he had already paid it to me earlier

I took a vacation in early July with about 3 days of vacation time I had left that my former employer had stated that I had left. About a month later, I gave my 2 weeks notice because I had received another job offer and my employer at the time didn't give me anymore work because his "policy" was to stop giving work to employees who quit. I worked as a PI and he was afraid that I would just stop caring and do a bad job. A couple days later I received a letter in the mail stating that he "fired" me even though I gave plenty of notice and he tried to make it so I couldn't collect unemployment for those 2 weeks, fortunately I was able to do so, and he sent me a check for half of what it was supposed to be. After a few weeks and getting in touch with the NYS labor board a sheet was sent to me explaining where my now former employer got the figure for my last check. He deducted about $400 from my last pay check saying that I actually had no vacation days, even though he clearly stated to me that I had 3 days left and he had already paid me for them. Can he do that?