apps deleted when syncing never happened bifore iPhone

Hi, Ive syncd many times but today my apps disappeared.
(Since previous sync, I had updated to iTunes 10.1.2.17)
I saw in discussions I needed to deliberately load purchased items in iTunes; I had never known that but had never had this problem.
I did have it set to sync automatically when I connect phone.
Does it mean I must have had box unchecked for sync apps
and when I updated iTunes, it reverted to a different state?
I found the apps are not in iTunes either.
All my apps had been loaded on iPhone, not through iTunes.
Is there a way I can get my apps back? (some paid, some free) Thank you. Ralphiel
Dell Inspiron 1501 Windows XP