I received the message "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?" message on my desktop

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!!!!!