The cover for Knuckles: Endangered Species #1 (a.k.a. Sonic the Hedgehog Online #244) was based off of the cover art for both StH #211 and #245, as well as a promotional image for Sonic Chronicles: The Dark Brotherhood.
In Memoriam: StHO #249 was dedicated to the writer's father, who passed away two years prior to the issue's release.
ASO was meant to be a comic version of Lost Hedgehog Tales, itself a What Could Have Been document for the Archie Sonic comic before the legal issues. This included starting at #237 (the first issue to show signs of the lawsuit), and having Hershey St. John be part of the Secret Freedom Fighters instead of Leeta and Lyco. However, since LHT went on indefinite hiatus and the staff wanted to make their own story anyway, ASO ignored the events of LHT, and began at #248.
The team at ASO had plans for a remake of Chaotix Quest — in which Rob o' the Hedge and his family were written out of due to copyright issues and replaced with other characters. However, the team decided to leave Chaotix Quest as is, with plans to reveal what happened to Rob and his family to be given in the future.
A story centering around Silver and Blaze was teased for Mobius Legends #4, but was not in the final release.
A Patreon account was planned for the comic at one point, but the plans were scrapped. Likely due to not wanting to run in legal trouble for trying to gain money off of what is essentially a fan project of an established series. note Considering how heavily protective Ken Penders is of his Sonic-made characters likely played a role in the decision as well.
Cubot's accent for #248 was intended to be a surfer dude's one. It was changed to a German one for the final product.
Plans for a Metal Silver was planned for #248, and it was even designed before it was cut out.
There was going to be more dialogue from the Secret Freedom Fighters in StHO #249, but they were either cut out or compressed. The only members who spoke in the issue were Elias, Shard and Harvey.
Amy was originally going to defeat Emerl by herself in StHO #249 instead of getting aided by Silver.