Do citations of the arXiv version of an article transfer to its journal version after publication? The arXiv version of my article has two citations. Now that my paper is published in a journal, I want to know if these citations will be transferred to the journal version? Should I withdraw my article from arXiv?
No, the citations will not change just because the paper is published in a journal (however, if the citations are themselves in preprints, then contacting the authors to make them aware of the publication would make sense, and would probably make them either update the citations in the preprint or at least change them for the final publication).

However, what you can do is update the arXiv paper to add a mention of where the paper has been published.