What Operating System? Have you goy iTunes version 11.2.2 installed. See this thread for earlier issues.
I assume your I pad has enough free space. My granddaughter creates a playlist of about 1200 songs for her iPhone to avoid overload so we set up iTunes to manually synch , and in the case of her I phone tell it to only synch this playlist. As long as everything is on your PC you will only lose the data on the iPad if you do a full restore, then you can re - synch it. I suggest you look at capacity first. I assume you are synching with a USB cable rather than iCloud / iMatch?