Denyer wrote:most of it technically happens in Joes continuity as well -- in that respect modern continuations haven't been direct follow-ons from Marvel.
My personal opinion (which is backed by some empirical data) is the while the Transformers stuff that occured in GIJoe #138-142 count in Joe continuity, the stuff that occurs in G2, even the scenes with GIJoe characters in them, do not count.
I look at their two continuities as parellel Universes which "dip" into one another at random points. IE, Transformers do not exist in the GIJoe Universe until the first Crossover, where the two Universes exist in the same space at the same time, for four issues length.
When that time is over, the Autobots, Decepticons, and the ancillary characters involved in the story go back to their own, separate Universe, leaving the Joes in a world without Transformers, even tho they remember the events that transpired.
Come 1993, the Universes cross once again, putting Megatron and Starscream on Earth to do business with Cobra (note that two robots are seen in 138, even tho only Megatron flies out to Trans-Carpathia). Because the Universes are now overlapping, GIJoe is able to send a message to Cybertron, and alert Optimus, who sends a small team of Autobots to Earth... most of whom are killed. At the end of #142, Megatron takes the Ark and Dr. Biggles-Jones back to Cybertron (we're shown specifically that they are in deep space at issue's end).
This is the point where the timelines once again split off. in G2 #2, Megatron never leaves Earth, and GIJoe agents successfully destroy a Cobra truck full of Ark Technology. Spike and Fort Max destroy the Ark, and Megatron barely escapes to reunite with Starscream and battles Bludgeon for leadership of the remaining Decepticons (G2 #4). In #6 or 7, Hawk and Flint finally meet up with Optimus as he attempts to confront Megatron about the Swarm and the G2 'Cons. In the meantime, the Decepticons have been wreaking havoc across the country, and Hawk looks to be on the verge of a heart attack when Optimus arrives. By the end of the series, San Francisco is destroyed.
In the GIJoe version, Megatron leaves in the Ark, and is never heard from again. Cobra's Ark technology is corrupted and made worthless by the same virus Dr. Biggles-Jones tried to infect Megatron with. With the battl over, Hawk, Scarlett, Rock'n Roll, Stalker and Snake-Eyes are picked up by the Tomahawk and taken to Washington to answer questions about Dr. Biggles-Jones. (This is major, since it implies the Doctor is no longer around to answer those questions herself, despite the Joes successfully rescuing her in G2 #2).
By the next issue, Hawk and Stalker are advising General Liederkranz in Wolkekukuckland with Flint joining them a few issues later. The end-of-the-world scenario played out in G2 never seems to occur in the Joe universe.
For my money, Larry Hama did his duty, and wrote the crossover as he was ordered by Marvel. When his involvement in the crossover ended, so did his obligation to include the aftermath in his book. By that measure, the events of Transformers G2 have no repercussions on the GIJoe Universe... when Megatron flies off with the Ark, the crossover ends as far as GIJoe is concerned.