Calling all parents- help!

I have so much blogging to catch up on...our cruise, visiting grandparents, grandparents visiting, visiting more grandparents... you get the idea! BUT in the meantime we need help over here! Many many months ago we did the whole sleep training thing. Eat, play, sleep...put him down awake...let him cry it out...blahblahblah. We quickly had our little guy sleeping through the night. Well a few weeks ago he got a yucky cold/cough/high fever. I, of course, didn't let him "cry it out" while he was sick and he got cuddled and held at night for several nights. Now he's ruined. After we determined he was well enough to get back on schedule, we let him cry. He's been sick in the past and afterwards it always takes a couple nights to get back to normal. After 5-10 minutes he cried until he threw up. So maybe he wasn't all better yet?? (He didn't throw up while he was sick mind you.) A couple more nights went by and he seemed completely recovered we tried again...threw up. Now everynight we put him in his bed awake he cries until he throws up (always only 5-10 minutes after we put him in). What do we do??! He's totally out smarted us, we can't figure out what to do. We can't let him sleep in his throw up...so what does that leave?? We are desperate for any ideas. HELP!