@Shankar - Not certain what an Alexa rank of zero would be.
I have tried a couple of things to deal with this. I had an Alexa of under 300K but after the .in redirect, it shot back to the 1M plus mark for both the domains.
I have broken my backlinks strategy into three parts, .com, .com/ncr and .in, and I rotate between the three when I am backlinking so that all of these are equally backlinked. The .com ensures that there are adequate backlinks to the .com domain, while the traffic gets split according to where the page is being viewed from. The .com/ncr helps pick up the traffic from India and other countries towards the .com domain without changing the domain suffix. The bulk of my traffic is India and US, and the .in backlinks helps keep the numbers up for that.
The problem is that every time I use a .in backlink and it is clicked on from outside India, it gives the viewer a page not found error. I have not found a solution for this. I am not certain if the rel=canonical tweak works for blogspot domains, since I have not tried it.
I have done this consistently (which is not a lot, but yes, consistently) for over six weeks, and now I have both the .com and .in domains back to the low 400s.
Any other ideas with anyone?