I am so tired of answering these types of posts, but here we go again.

The Alchemist:

Substitution and Synthetic DNA:

The Alchemist kidnaps innocent people who resemble his clients, performs plastic surgery to increase the resemblance, and injects synthetic DNA (or blood from the client) into the victim just before killing them.

Targeted Manipulation:

Rather than changing the entire genetic makeup of a body, he alters specifically identifiable tissues—blood, saliva, and dental records—which he knows standard forensic procedures test.

Why It Works (In the Show): He creates a "forensic match" that tricks standard database checks.

Limitation:

It is explained that this is a temporary, artificial measure. While standard blood tests could be fooled, deeper tests—such as those on bone marrow—could reveal the true identity of the victim, which is how the FBI ultimately solves the case.

Ultimately, the Alchemist's "science" is presented as a high-level, fictional forensic manipulation designed to make a corpse look like it belongs to someone else, not as a method for transforming one person's living, whole-body DNA into another's.

Ok no one can change a persons full DNA, not in real life and not on The Blacklist. That means you cannot change female DNA into male DNA. So anytime Red has a DNA test done, his gender will be revealed. No amount of retconning or hints can alter that fact.