As an aside, is this in the right forum? I have a feeling it should be moved to the AH Books and Media section.
*SPOILER ALERT*
The Link
I have and I quite liked it, even if having both Lee and Thomas in Texas at the time is a bit of a stretch.
As for some thoughts on how the war would progress in such a scenario
-Thomas' presence at the Alamo is going to cause his star to rise tremendously. As one of the war's first heroes for the Union I'd imagine that he'll be treated much better and be given a fairly major command sooner rather than later. He might even end up staying in Virginia as after TTL's actions at the Alamo his loyalty won't be suspect. I can't see a whole lot of downsides to this save for that Thomas' caution could get him blacklisted by Lincoln.
-Lee taking a command in the West will be interesting depending on where he ends up. His movement over there could very well precipitate a major reorganization of the theater. One interesting possibility could be that Lee succeeds Anderson in the Department of the Ohio and launches an offensive down into Eastern Tennessee to relieve the Unionists there...How effective that would be is anyone's guess. Perhaps Thomas comes along for the ride?
Another possibility is that Lee prompts a much earlier reorganization of the West. Lee could be given responsibility for the entire Western Theater while Halleck becomes General in Chief in Washington (he was Scott's preferred candidate not McClellan) while Lil' Mac is limited to command of the Army of the Potomac. In such a scenario I could see Thomas being put in charge of an offensive to relieve Unionists in Western Tennessee.
Lee's absence from the Confederate cause would also have ramifications. Not all of which would be horrible.
-For example, Lee was assigned to command the department of South Carolina, Georgia and Florida in late 1861 in OTL. During his tenure he ordered Tybee island to be abandoned which the Federals later used to bombard Fort Pulaski into submission. Perhaps in TTL his replacement (perhaps Beauregard? He did a pretty good job earlier...)doesn't make the same mistake thereby keeping Savannah GA open as a port for longer.
-Lee also convinced Davis to transfer Ewell's brigade to Jackson in the Shenandoah instead of honoring Joe Johnston's request for troops. In TTL his successor might not. Without Ewell Jackson is probably going to be overwhelmed by superior Union numbers in the Shenandoah.
As you progress further into 1862 the butterfly effect begins to change things and the results of 1861 begin to stack up.
One interesting possibility in TTL could be the war ending earlier, prior to November 1864. Lincoln in an effort to unify the country picks Lee (who perhaps has freed his slaves in TTL) as his running mate instead of Andrew Johnson.