From NXE 2:9

Misato looked curious. "You sound like this has happened
before."
"It has," said SHODAN before Ritsuko could interrupt. "In
2005, before you came to NERV, the unit absorbed its original test
pilot. The process I described was developed in an attempt to restore
her."
"Did... did it work?"
"No," Ritsuko said, scowling in the direction of SHODAN's
sensor pickup. "It didn't. That's what makes EVA-01 different from
the others, Misato... it has a human soul."
"Two of them, now," SHODAN said dispassionately.

I had assumed, from other NGE sources, that Yui was the original test pilot. Of course, that was required for Shinji to pilot EVA-1. Here in NXE, Unit 1 needs to synchronize with Longinus since it contains (actually, is Lucifer, half smote (smitten?) with the Lance.

SHODAN noted that Yui was absorbed into EVA-01, very similar to the way Longinus was. This implies that Lucifer had communication with Yui. SHODAN also notes that they failed to recover her.

TMP tells us that Yui was murdered, in 2004, by Natla. How is never mentioned, except that she was completely destroyed.

So my two questions:

1: If Yui was absorbed "to death" by Lucifer, how did she end up in SHODAN?

2: If Yui wasn't absorbed, who was, and where is she now?

--rR