There are only a handful of things that this might impact.
The spell 'Insecticide' from the Street Grimoire was developed after the initial Bug City incident
The Bug City incident was the big trigger behind the massive fear and paranoia around Bug Spirits that exists in modern Shadowrun....but that's pure fluff and can easily be ignored.
Likewise, in terms of fluff, Ares Reputation took something of a hit when it was discovered that FAB Strain III targeted anything that was astrally active, and thus killed a bunch of ghouls.
Other than that...while the events of the Bug City may have had an impact on the overall cultural climate of the world...it didn't directly impact very many things. You should be able to make this shift pretty easily if you want your players to get to experience the fall of Chicago.