Here's the retcons I remember on the corporate front. Past the two first items, that's is mostly very minor stuff.
In Seattle Sourcebook, the section on the Seattle United Corporate Council wonder if the corporations of the world may be "secretly building a global organization through which they hope to influence, it not control entirely, the planet's governement". While Corporate Shadowfiles barely touched the issue of influence over governements when it introduced the Corporate Court as a global organization whose existence was widely known, Corporate Download has the megacorporation pushing for ratification of the Business Recognition Accords as early as 2042, making the need for a secret organization dubious at best.
In Seattle Sourcebook, Aztechnology and MCT have corporate warships - the Tezcatlipoca and the Izanagi. In Corporate Shadowfiles, Aztechnology is said to have zero military assets and MCT has only a company-sized military force (which would ne be enough to staff a warship). That was completely reverted in Aztlan regarding Aztechnology, whose armed forces were said to be three times as large as the national army of Aztlan, and a number of subsequent books. Overall, Corporate Shadowfiles is pretty much the only book where corporate forces are described as that small.
As a side note, Aztechnology headquarters was said to be in "Mexico City" in Seattle Sourcebook and Corporate Shadowfiles (that is, until the release of the Aztlan sourcebook established the Aztlan capital was renamed Tenochtitlan).
In Seattle Sourcebook and Corporate Shadowfiles, Ares Arms Military Systems Division maintains extensive military asets within the Ares Macrotechnology group. Since Corporate Download and Year of the Comet, Knight Errant Security Services has been providing military forces.
Yamatetsu, Cross Applied Technologies or Phoenix Biotechnologies were completely absent from Seattle Sourcebook, The Neo-Anarchist Guide to North America and Native American Nations.
On the other hand, The Neo-Anarchist Guide to North America mentions Cord Mutual as the largest insurer in the world. The corporation then never appeared for years (that's the case for many other corporation, but Cord Mutual was one of the only ones to be specifically ranked a world leader).
The Atlantean Foundation was listed as one of Seattle ten largest megacorporations in Seattle Sourcebook, as a major player in awakened employment. It was not listed in the similar chapter in New Seattle or Seattle 2072.
The foundation was headed by Casey Williams in Seattle Sourcebook, then founder Sheila Blatavaska in Dunkelzahn's Secrets: Portfolio of a Dragon and Loose Alliances (with Williams as a boardmember) then again by Williams in Dirty Tricks, in which it is said there is no record of him before 2051 (Seattle Sourcebook being set in 2049...).
Weapons World was introduced as an independant company in Seattle Sourcebook. In Corporate Shadowfiles it was a subsidiary of Monobe International. In Corporate Download it became a subsidiary of Ares Macrotechnology. Then in Corporate Guide it was again a subsidiary of Monobe International.
Shin Chou Kyogo produced the SCK 100 submachine gun introduced in the Street Samurai Catalog. In Corporate Guide, it is described as involved "in social research and the creation of a compete (sic) record of human history".
In London Sourcebook, the Fuchi top executive in Great Britain was Charles Nakatomi, an anglo-japanese whiz-kid of the Nakatomi family. Later books, including Corporate Shadowfiles and Blood in the Boardroom, established the Yamana ran Fuchi Pan-Europa and the Nakatomi ran Fuchi Asia.
In London Sourcebook, Zeta-ImpChem owned Hoechst AG, who also became a member company of the AG Chemie consortium in Germany Sourcebook. German-only books retconned the name into Hoechst-Aventis after Rhône-Poulenc and Hoechst merged as Aventis in 1999, a name that was also used in Shadows of Europe. Corporate Guide retconned the name again as Sanofi-Aventis, since Sanofi-Synthelabo took Aventis over in 2004.
The Renraku European headquarters was in Paris, France, according to the Germany Sourcebook. In Corporate Download, the HQ was recently moved to Munich because division head Karl Stadt couldn't stand the anarchy of... Berlin. Also Corporate Download does not list any prominant facilities in Paris.
The Aqua Arcana company was founded by one Jebediah Jones according to California Free Statet. In Hazard Pay, there are three founders, Isabel Madira, Michael Paul and Alexander Greyson.
In Shadows of North America, the Saeder-Krupp North America headquarters were in Charlotte, CAS, and S-K had yet to be allowed to do business in Tir Tairngire. Seattle 2072 mentions that S-K still had no business in Portland. In Corporate Guide, Saeder-Krupp North Am HQ were in Portland, Tir Tairngire. Dirty Tricks acknowledges the existence of the Portland and Charlotte facilities, but says the Charlotte HQ was established after Portland, "when the Tir troubles started," which would imply S-K was operating in Tir Tairngire as early as 2057.
James Haper-Smythe, boardmember of Wuxing, was 32 years old in Corporate Download. Nine years later, he was "the other old man of the board" in Corporate Guide.
Tsuruga International, one of the founding parties in Yamatetsu, was an international shipping company according to Blood in the Boardroom and Corporate Download. In Corporate Guide, it was described as dealing exclusively in road construction.
Trans-Latvia Enterprises was a Latvian company in Shadows of Europe. It was a Estonian company in Corporate Guide.
In Vice, the top five corporations in security were Ares Macrotechnology, Lone Star Security Services, Wolverine, Centurion and Eagle Security. In Corporate Guide, the top ten were Ares, Lone Star, Maersk, MCT and Yakashima Technologies, Renraku, Pueblo Security Enterprises, AG Chemie Europa, Esprit Industries and HKB.