I'd be the first to admit that there's no actual crossover here. But considering the overwhelmingly Chinese flavour of the book, and the fact that The Years of Rice and Salt does just happen to detail the exact right time periods for Feng Shui - the 1850, 1996 and 2054 junctures, here's one way it could work:

 

The Critical Shift

It all starts, as Feng Shui so often does, with a Critical Shift. Even in the novel, no one's really sure what made the great plague so virulent. In the world of Feng Shui, it's likely to have been someone's attempt to upset the balance of things. Front runners include any opponent of the Ascended, since keeping the Ascended out of Europe would effectively dethrone them in both the 1850 and 1996 junctures. My guess is that it was the Jammers using stolen, and poorly-understood Architect technology - such a large and conspicuous destruction seems their kind of overkill. It's also possible that the plague was a desperate attempt by the Lotus to wipe out all of its future competition in one fell swoop. It doesn't really matter who did it, or even why - although it's likely that they were caught in their own scheme and infected along with the rest of Europe.

The effects were profound. Thousands of Innerwalkers were serially reincarnated - but for many of them, their actual ancestors were wiped out for many generations. This mostly applied to Innerwalkers of Causcasian descent - most of whom found themselves to be citizens of the British Isles, in this timeline a small and irrelevant nation following a mixture of Christianity and Celtic pagan religions, until it is absorbed into Dar-el-Islam.

Innerwalkers of Negro descent most often found themselves in one of the patchwork of Islamic states that covered Africa, while Amerindian Innerwalkers usually discovered that their backgrounds in the new timeline were considerably wealthier. Most Asian Innerwalkers were not as greatly affected - the histories of their families were more or less intact.

The Ascended, who had bet on Europe to beat Islam, were rudely surprised. Although they retained much of their power in Asia, their Western arm was almost completely destroyed, and what remained was forced to flee to the Netherworld - which spread the plague there, too.

Even worse off were the Architects,their future erased completely from the timeline. For a time, the remaining Architects and the Jammers battled to the death in the Netherworld, and a lot of Arcanowave technology turned up in the Inner Realm's black markets. After a few months, both sides were too exhausted to fight much further, and so reduced in numbers and power that they were having trouble finding each other. Within a generation or two, both factions will probably die out completely.

 

The 1850 Juncture

The 1850 Juncture is not ruled by any one faction. While the Ascended have a toehold in Britain, and the Dragons have some influence in the lands of the Hotisavannah League, Dar-el-Islam is still largely untroubled by Innerwalkers or the Secret War. Meanwhile, power struggles within the Chinese government between the Guiding Hand and the Lotus have only worsened the endemic corruption and innefficiency of the system.

If anyone can be said to have ascendance, it is the Dragons, who have based themselves out of Travancore, and who are the only faction to really have a global perspective. Indeed, Travancore in this world takes the place of Hong Kong as the location where pretty much anything goes in terms of the Secret War. To both the factions of the Secret War and the more mundane factions of the world, Travancore is, by virtue of its location and its political alignment, a more or less neutral territory - albeit, one with an agenda of its own and the will to see it acheived.

 

The 1996 Juncture

The great War of the Asuras ended only 17 years ago, and its shadow lies heavy over the world. In the end, it didn't change a thing. The Guiding Hand solidified its control over the Chinese portion of the world, squeezing out the agents of the Lotus ever more assiduously, while the Ascended regained lost ground by finally managing to seize control of Dar-el-Islam.

After the war, there's a long, slow peace. The Dragons, still based out of Travancore, work carefully and quietly to ensure this peace, using politics and economics rather than force to capture vital feng shui sites, and frequently beating the Ascended at their own game.

Simmering tensions from the War of the Asuras mean that mundane politics frequently intrudes on the Secret War - many feng shui sites have been lost as a result of the long battle, particularly in middle Asia where the worst of the fighting took place. And the desperation of both sides to perfect unstoppable weapons has led to a development of some limited Arcanowave technologies, all combat oriented.

 

The 2056 Juncture

The survivors of the Guiding Hand, cheifly those who were moderates, have renamed themselves the Pointing Hand, and are determined to use evangilism rather than force. In fact, they've more or less merged with the Dragons by this time, and the patient work of both factions is turning the tide in their favour. While the War is long over, no one has forgotten it. Instead, peace and progress are the order of the day.

The slowly rising level of technology has made the Architects something of a threat again, although their Arcanowave technology is vastly less reliable than it used to be. Still, the ideas of the Architects are appealing to a world that still has nightmares about the war.