This is the timeline that I'm using. It's still a work in progress, as some eras are bare. The rule of thumb though, is that anything not mentioned is unchanged from canon, or close enough not to matter. Please don't hold back on the feedback here: this may be a 20-year update, but a lot is still possible.
timeline:
3043: with the creation of the LGAO, the FWL industries begin a massive increase in production, through sales to Kapteyn and Periphery allies. The economic boom experienced in canon due to the clan invasion happens instead due to its Kapteyn allies (and a few years early).
3048: World after world goes silent in the Periphery, as pirate bands begin to disappear. While in canon this is a result of Operation Revival, in this timeline it the beginning of the reformation of Rim Worlds Republic.
3050: Romano Liao assassinates Justin Allard, as in canon except for occuring a year early, setting off Hanse Davions's attempt to finish off the Capellan Confederation.
3050-3052: Due to arms shipments by FWL industries, interference by ComStar, and sheer Capellan stubbornness, Hanse Davion's forces are unable to conquer the CapCon, as battles bog down on every world.
Victor Steiner-Davion, originally stationed on Trellwan, gets his trial by fire when the Draconis Combine enters the fray, hitting Trellwan with the 11th Legion of Vega. Combine forces also stage deep strikes on Tamar and Coventry. FWL forces stage probing raids along the border, but do not commit any great number of forces.
At the same time, forces of the newly recreated RWR (in reality, a coalition of forces from the Oberon Confederation, Von Strang's world, and the recently united Chainelaine Isles), equipped and supported by the FWL and ComStar, begin a surprise invasion of the Lyran commonwealth, capturing Apollo and six other worlds by late 3052.
3052 : As in canon, the extraordinary effort of fighting a war that goes entirely against him proves too much: Hanse Davion dies at his desk watching a holovid sent by Sun-Tzu Liao (who ascend to the Celestial throne in the manner and time as in canon). Operations wind down, and both sides return to pre-war borders. In all, the biggest losers are mercenary forces, who suffer staggering losses (equal to those suffered in the canon clan invasion).
3052: Myndo Waterly, Primus of ComStar, is 'removed' from office by Anastasius Focht after the failure of Operation Scorpion (as in canon, an attempt to capitalize on the confusion caused by the current conflict). No details ever emerge from the meeting with the first circuit, except to announce the ascension of Demona Aziz to Primus.
3053-3057: no significant deviations from canon; an enormous amount of politicking, esp. in the FedCom, occur. The FWL continues to grow due to the economic boom caused by arms exports to the Combine, CapCon, and various Periphery nations.
ComStar, still suffering from the backlash of Operation Scorpion, works tirelessly to rebuild its image and regain the trust of the Inner Sphere, although is only partially successful. It is successful, however, in concealing an increasing radicalization within the order.
3057: Operation Guerrero. Even without Joshua Marik on New Avalon, Marik and Liao still go ahead with the invasion.
3058: First Whitting Conference, an attempt by Comstar (almost completely Word of Blake by this point) to negotiate the reformation of the Star League. Results are disappointing, as the only agreement reached is cooperation against external threats.
3058-3062: TBA
3062-3067: FedCom Civil War. Largely unchanged; both halves are battered into the ground.
3067: Second Whitting Conference, the ongoing attempt by Comstar (completely Word of Blake at this point) to negotiate the reformation of the Star League. The rejection of the proposal by the various houses sets the stage for the Jihad.
Chandrasekhar Kurita sends the Devil's Brigade mercenary unit to New Dallas, returning with the Hegemony Memory Core (never clearly stated when it occurred in canon).
3068: Dawn of the Jihad. Strange, almost alien forces appear from nowhere to attack Luthien, Tharkad, Northwind, Solaris VII, Canopus, and Atreus. Calling themselves 'Jade Falcons', 'Clan Wolf', 'Smoke Jaguars', to name a few, possess a level of technology rivaled only by ComStar and the original SLDF, matched to unbelievable skills.
3069: The Jihad intensifies, as more of the so-called clans enter the fray. The combo of high-tech weapons and dazzling skills proves too much, and world after world falls to the nigh-alien enemy. It is at this time, however, that The Secret (see below) leaks to the Inner Sphere.
3070: The Jihad continues unabated, although the tide begins to shift against the invaders.