Does phyrexian mana count toward a spell's converted mana cost if paid with life?

A spell's mana value (the official term replacing 'converted mana cost' since Magic 2021) is a property of the card itself, calculated from its mana cost as printed. It is determined before any payments are made and is never affected by how you choose to pay that cost. This is established in CR 202.3.

Each Phyrexian mana symbol (e.g., {W/P}) contributes exactly 1 to the card's mana value, per CR 202.3f. Whether you pay that symbol with one mana of the appropriate color or with 2 life, the symbol's contribution to the mana value remains 1 either way.

This means a card like Gitaxian Probe, with mana cost {U/P}, always has a mana value of 1 — even if you paid its cost entirely with 2 life and spent zero mana. The method of payment is irrelevant to mana value calculation.

Concrete example: You cast Gut Shot (cost {R/P}) by paying 2 life instead of {R}. Its mana value is still 1. If your opponent controls a Chalice of the Void with one charge counter (which counters spells with mana value 1), Gut Shot will be countered regardless of how you paid for it.

In summary: Phyrexian mana symbols always count as 1 toward mana value, and the chosen payment method (mana vs. life) has absolutely no effect on that calculation.