I'm trying to remember if Alain was gone in 2004 by the time "How Soon is Now?" got added into the live rotation. I think he was.
At the time, his departure from the live setting seemed only to be temporary. Some of you long-timers might remember when Boz would post a diary of sorts on his website. There were multiple entries mentioning Alain between July and September of 2004 which were later excised. I am "paraphrasing with loose quotes" here, but the first arrived shortly after the Chicago House of Blues show - Jesse's first - in which he said "Alain's illness was apparent." I can't recall if it was before Reading in August (where "How Soon Is Now" was first played in a solo show) or shortly before the second US leg of the
Quarry tour kicked off in September, but he wrote an entry about Alain stopping by Lyn's coffee shop and "looking fit and raring to play" or something to that effect. To my recollection, Boz never mentioned him again on any further updates. He did later answer a fan question at one point asking him to compare working with Jesse and Alain and it was a vanilla response (i.e., "different but both great").
I had gleaned - and later had confirmed by people who talked with Alain during the Red Lightning period of 2005-2007 - that he took time away, got better (physically and/or mentally) and anticipated returning to the band in full capacity in fall 2004. When that didn't come to pass, he put all his energies into Red Lightning. It is notable that Alain played a quite capable version of "Bigmouth Strikes Again" at some of their live shows after the recording of
Ringleader, which may have been cocking a snoot at any assertions that he wasn't capable of handling the Smiths material and, what's more, using a song that Morrissey and Co. played frequently in fall 2004.
Alain seems to have found his happiness in his family, gets to pick and choose the songwriting work he does, and has the luxury of playing with other musician friends in a low-key side project. He has also implied on Facebook in the not-too-distant past that he is preparing to release solo material. In some ways, leaving Morrissey behind seems to have opened the door for him to be quite happy. Good on him.