This user tip may help too
I must tell you, I am in the situation that MegsiPhone described and I am confused as to what to do. Here is what I have done thus far:
1. I installed iTunes on my new computer, I wen't ahead and set up a new library file locally, and pointed to my NAS for all the music and movies file in edit>advanced. From what I recall, when I did I can remember getting a whole bunch of messages about apps, new versions, overwriting. I don't recall, regadless I dismissed each on and did not override. Anyway, that's all done now.
2. I can tell you that I used to back up three iPhones and an iPod touch to my old PC. There is a mixture of 4 iTunes ID's with various app purchases, it seems a mess.
3. I did plug my phone in, it gave me the error message about syncing only to one computer. Then I did a back-up and a sync. I know it did not work right because it took a matter of seconds when I know it should take a lot longer. Anyway, as a safeguard I am using iCloud back-up for now before I do anything else.
So, what do I do now to make this all right? I would like to be able to sync mine and my wife's iPhone to the computer. Should I not bother and just keep my back-up in the cloud and are there disadvantages to this? For my son's iPhone, I can let him back-up to the old computer, I would assume that would remain good and I would not have any issues. Should I erase the back-up on my new computer, erase the appss or whatever and start from scratch? Kind of not sure how to handle, please help.