Interesting...

I have my own theories about these two episodes as mentioned in my anal-ysis:

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[From "Box" review...]

"Six Kilos," now the 22nd show, was originally 18th in production order, before this one, which was 21st, now 16th, and before "Six Kilos."

One of the four major characters in "Six Kilos" is Carl Swanson, an "expert electrician," part of a safecracking team played by O'Loughlin. At the end of "Six Kilos," Swanson is shot by that episode's villain Margi (Antoinette Bower). The episode wraps up and we are not told of his fate, but in "The Box" we find him, having survived, again a major character, now in Oahu State Prison under the name of Charlie Swanson.

In other words, Swanson is in jail in this episode before he is busted and sent to jail in "Six Kilos," which is now later in broadcast order.

In an interview with the Archive of American Television (available on YouTube), Gavin MacLeod says because his previous appearance as Big Chicken in S01E05 was such a smash success, the producers told him, "We want to write another one for you at the end of the season [emphasis mine]." So it was really intended that Swanson should be in jail because of "Six Kilos," and "The Box" would have appeared after that show.

See also the discussion for S01E21, "Not That Much Different" and S01E22, "Six Kilos," below.

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[From S01E21 discussion]

There are hints of homosexuality between West and Julian when Horvath confronts West with the letter the latter wrote to Julian. West refers to his "affection" for Julian, adding later "I loved him," holding the letter up to his face as if he is kissing or smelling it.

I suspect that the homosexual relationship in this show was originally played up more, and the bigwigs at CBS told the production team to dial it back. In the episode "The Box" earlier this season there is a reference to "homosexuals" in prison which was probably pretty rank enough for the era when Five-O was broadcast. Perhaps this stuff was edited out at the last minute and the script revised, which is why it is such a mess.

It is also possible that this gay angle was responsible for changing the order of episodes close to the end of the season (this is my theory).

Consider the following. In production order, "The Box" and "Not That Much Different" were separated by only one show. Both had "homosexual" references.

In broadcast order, "The Box" and "Not That Much Different" were separated by four episodes. Not a lot, but perhaps the best that could be done by the time the broadcast order was determined. Moving "The Box" around in this manner actually screwed things up, because in "Six Kilos" there is a character named Swanson who is shot and wounded, and he later appears in "The Box." In production order, these two episodes were in correct sequence. But after "The Box" was moved to episode 16, Swanson, who was shot at the end of "Six Kilos" is first in prison in "The Box" where he would likely be staying for a long time.

PRODUCTION ORDER:

Six Kilos #18
The Big Kahuna #19
One for the Money #20
The Box #21
Face of the Dragon #22
Not That Much Different (last produced episode) #23

BROADCAST ORDER:

The Box #16
One For The Money #17
Along Came Joey #18
Once Upon A Time, Parts I & II #19 & #20
Not That Much Different #21
Six Kilos #22
The Big Kahuna #23

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My review of Six Kilos (S01E22) has a copy of the “final draft script” of that show…