-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.