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So does that mean Cytodyn has to create a separate response to FDA’s questions on the HIV BLA?

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The issues for a safety hold would differ from those in setting up a trial protocol although approval on a protocol would hinge on the safety hold being lifted. There would be different processes for both.

The FDA wouldn't have asked for a protocol unless they knew they were going to lift the safety hold. It might be a way for the FDA to pressure Cytodyn into an HIV trial after Cytodyn said they were abandoning HIV.
Some in the FDA must know what maraviroc can do and what leronlimab with 100% CCR5 coverage and minimal side effects is capable of in HIV. Now they just have to be educated in what leronlimab can do outside of HIV.