Let me set this up:
You had an e-mail you used to log-into Bungie.net, because that WLID (Windows Live ID) had your Xbox account and Bnet account linked, correct? Then you wanted to change the e-mail you used and logged in with to another e-mail.
You changed the e-mail from your Xbox/Xbox.com, but this just unlinked your gamertag and to log into your Bnet account you still need to use the old e-mail address (WLID). You want to have your gamertag linked, but be able to log in using the new address.
If this is incorrect, please disregard the following completely. If my above analysis is correct, then I'm going to refer you to this post I made earlier today:
Been there. Done that. Most people think that what you want can't be done. Common misconception.
You CAN change everything to how you want it... but you will need to wait the 30 days, sorry. Here's what you do.
Wait the 30 days. Then from your Xbox, change the e-mail BACK to what it was. This will relink your gamertag. Then go to the windows live ID website. Log in using that old e-mail (since you just changed it) and password. At the top right should be something that says 'change WLID.' Put in the new e-mail. This will change the WLID on your Xbox AND the one used to log in, but it won't unlink your gamertag. And no, I have no idea why doing it on the website is different from on the Xbox. Probably something to do with it only switching it for the XBL accounts or something. Oh, also you don't have to wait another 30 days to do the Website switch.
Whatever. Just do it in the steps I listed. If you do it out of order... not sure what will happen to be honest, hah. But I've been in your shoes. For the next 30 days you'll just need to put up with not having a linked GT, sorry.