Crossposting here from DCW since I don't think I am going to get too many on topic responses. Since the new plot developments with Kohji's death, I have very slowly worked on several APTX-related theory sections in prep for updating the main Chek's theories document.
The two main endeavors are 1) the Unknown Drug page
alleging the existence of a drug older than APTX 4869, Silver Bullet, and the Miyanos, which is still in need of additional content, and 2) A theory that Shiho's APTX 4869 version is contaminated with research from Silver Bullet
which adds additional nuance to my APTX purpose theory and attempts to reconcile the other drug Shiho was asked to develop and why the Black Organization is using an untested drug for killing.
I would very much like it if someone would "beta read" and make suggestions regarding the second theory (the X-Contamination theory). Here it is posted below.Shiho's APTX 4869 version is contaminated with research from Silver Bullet
It is known that the APTX 4869 of 17 years ago was used for murder and that Shiho's current version of APTX 4869 is being used for the same purpose. It is unlikely that the generally cautious Black Organization would use a custom drug for murder if they knew it had a chance of shrinking the victim and leaving them alive. It also doesn't make much sense that they would kill people using an in-development drug which Shiho explicitly stated was not created for murder and which is suspected to have a somewhat miraculous end goal such as deaging, rejuvination, or immortality.
This contradiction can be explained by the Black Organization mistakenly operating on the assumption that Shiho recreated her parents' APTX 4869 (which may have been tested in the past and found to kill exclusively). It is known that a lab fire destroyed most of Elena and Atsushi's drug project research. Shiho had to piece their research together from fragments. It is certainly possible that damage from the fire destroyed certain context clues that would allow Shiho to figure out which research belonged to the APTX 4869 drug, and which belonged to Silver Bullet. In resurrecting her parents' work, Shiho mixed the research together. This hybrid is the modern APTX 4869.
Perhaps because the project took the name APTX 4869 rather than Silver Bullet and for the most part has similar deadly results, most of the Black Organization seems to have assumed that it is the same drug as before. Their ignorance can an least be partly explained by Shiho hiding certain results so that even executive members of the Organization were not aware APTX 4869 could cause de-aging. It is possible Shiho may misinformed the Organization about the status of her recreation project, not having realized she had mixed the research until after the Organization intended to use it for killing.
This mix-up explains certain conversations, such as the one with Conan about APTX 4869's history which implied the existence over another drug beyond APTX 4869. Haibara
: And the fact that [Kohji Haneda's] name was on the list of victims who were given APTX 4869, I'd say there's a good chance that Asaka was one of the members of the Black Organization! Conan
: I don't get it. Kohji Haneda was killed 17 years ago. Then why is his name under mine in the list? Haibara
: Perhaps the person who compiled the list wasn't going by chronological order. Maybe it was sorted by blood type or something. Conan
: Wait a minute, so the drug that I was forced to take existed 17 years ago? And you are its creator? How old are you really? Haibara
: How rude. I've told you before. I am 18 now. Perhaps it was an early prototype of a drug made by my parents. The information for the drug that I created was mostly taken from the burnt remains of the data that my parents left behind. Conan
: Burnt remains? What do you mean? Haibara
: Well, the research lab that my parents worked in caught fire, and along with them, most of their research materials were burnt. I heard from the other members of the Organization that it was an accident.
Well, what I was really ordered to make was another drug, however...
—Manga Volume 89, File 11 (948), Pages 3-4: "The Clenched Scissors"
In this conversation, it makes the most sense that the Black Organization was hoping that Shiho would not work on the prototype APTX 4869 used to kill in the past and instead recreate her parents' final project Silver Bullet which seems to have fallen through (perhaps by catching fire) before being completed. They gave these orders unaware that Shiho actually did what they wanted her to do, which in turn explains why Shiho said that she did not intend to create a murder drug and protested that the drug was used for killing. Instead, the Black Organization seems to mistakenly believe that Shiho had reassembled the prototype APTX 4869 of the past.
This type of development would be so very in character for Gosho, since it involves a significant degree of failing to share information and lots of secret keeping between supposed allies.
 Kohji Haneda's murder
 Gin's attempted murder of Shinichi, Pisco's backup murder plot
 a b Manga Volume 18, File 9 (179), page 9: "The Girl Made Of Lies"
 Shinichi's survival for sure, and possibly the one shrunken mouse which was tested. The most significant proof is that no one has figured out Shiho shrank to escape her handcuffs and the locked room. Someone aware of shrinking results could easily extrapolate what happened.