I have been having issues manually syncing between my desktop, iphone, and ipad. Nothing would manually sync and I am not in the Cloud. I found a link to resolve the initial syncing problem - http://support.apple.com/kb/TS1627. This fixed the manual sync problem and I was able to sync my ipad with the desktop. I then tried syncing my iphone and this worked a few times. Then after about 3 syncs the message above popped up on the desktop - iTunes will no longer sync apps to the iphone xxxx xxxx's iPhone". Do you want to keep or remove existing apps installed on your iPhone?". There were three buttons - Cancel, Remove Apps, Keep Apps. I chose the options "Keep Apps". I don't know what to do now!!!! Please help!!!!!
iPhone 4S, OS X Mountain Lion (10.8.2), iTunes manual syncing