Is it wise to resubmit a substantially revised version of my writing sample that has already been submitted for phd applications review?
One of three things will happen, depending on how far past the deadline you are and on the application management system used:


The graduate school will reject it without forwarding it to the departmental admissions committee. See Plan B below.
It'll be forwarded as supplementary information rather than replacing the original writing sample. Some faculty will see it, some won't get that far in your file since these are usually last in the packet.
It'll replace your original sample.


You don't have much to lose, so why not send it in and see?

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PLAN B

If the graduate school rejects your submission AND you've already been corresponding with a faculty member who would likely be your advisor AND those interactions have been positive, then you could suggest to that person that you could provide them a revised sample to share with other faculty.

If I were that faculty member AND if I thought your candidacy were strong AND my departmental and university regulations did not forbid out of channel submissions, then I might accept it that way. 

A lot of ifs with Plan B.