-Black Swordsman had a ton of Silica flags cut out in the final version. Kirito had carried Silica back to town after the attack in a 'princess carry' style and used his agility to run all the way. Also a exchange where Kirito teased Silica that yes, 90% enemies in floor 47 are indeed tentacle plants
As per other WEB stuff, the heroine (Silica) has completely fallen for the Hero (Kirito) but because of some reason cannot be with him and end up emotionally devastated by this fact. Kawahara likes his suffering... >.>
There was also a fix-up of the gear Kirito carried in the LN version, that it's unisex gear. There was much snarking in the Chinese fandom that Kirito might have been a pervert carrying around female gear for no reason
In the Web version Kirito didn't know Suguha was his cousin.
-No major changes in the one with Yui. Another major flag with Asuna and Kirito being all lovey-dovey, a section on Kirito musing in the future the physical world may be obsolete and everyone will spend their time in VR worlds due to less hassle, and Asuna being even more pissed at the Army minions and giving them a good thrashing.
-Red-nosed reindeer: fixed a plot hole that Kirito only met Klein 3 months ago in one of the floor-clearing meetings. Sachi was a childhood friend of the Guild leader of the Black Cats, but this was taken out in the LN. No major changes.
-Warmth of the heart: Hoo boy. Kirito was even more of a
womaniser Eroge protagonist here, flirting unintentionally with Lizbeth. Fanservice has been much reduced in the LN version, as due to the cold Lizbeth shared the same sleeping bag as Kirito in only her underwear. The title "warmth of the heart" was about them literally feeling the warmth of each other's heart via torso/body contact, not metaphorical like in the LN version. Borderline R-18 romance flags have been set, with Lizbeth thinking if Kirito had asked she would turn ethics mode off and do it with him right then and there.
(And there's a Side Story equivalent to 16.5 only with Kirito having sex with Lizbeth instead have been done by the author but not in this SS; I've found the section in Japanese, no Chinese translations anywhere AFAIK however. Would be nice if a translation existed in English/Chinese since I can't read Japanese- *shot*)
On other matters, Lizbeth needs to wear glasses IRL in WEB version, and she also used to have braided twintails.
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Spoiler for NSFW:
While searching for the Lizbeth R18 scene, I've also came across the R18 section where Kirito is seduced by Sakuya and Alicia (the Slyph and Cait Sith leaders in the BakaTsuki pic
here) with them calling Kirito to them on the pretense of planning the assault on the World Tree; in actuality it was to make Kirito theirs in ALO politicking. Yui got fed a 'non-alcoholic' drink, but it produces drunkenness status; with Yui KO'd this left Kirito to be ravished by the two leaders. Again, no English/Chinese translations available AFAIK, and my Japanese isn't good enough to understand much else.
Such a shame though ;_; *shot again*