Recently I've been having a big, annoying problem:
I store my library on an external hard drive. But I don't have it plugged into my MBP at all times, so some apps, music, etc. get downloaded locally. No worries, I consolidate regularly, all is good.
But recently (and it didn't do this in months past), when I sync my iphone without the external drive plugged in, it deletes the apps off the phone that are not in my local iTunes library. To fix this, I have to get my drive, sync again, and then go clean up, delete, and rearrange the apps to get things back to normal again.
Maybe this is a common issue, but this is the first time I'm seeing it. In the past, what wasn't on the local computer iTunes directory structure was simple ignored during sync. i.e. if the app wasn't on the computer, it did NOT get auto deleted off the phone.