Syncing apps to new computer and saving data iPhone

Hi,
I had to recently buy a new computer as my old one crashed. After plugging in my iPhone to the new computer, I authorized it and transferred all of my purchases onto it, I then backed up the iphone. I want to sync the apps now, but when I do it says that all the apps and the data will be erased and replaced with the ones on the computer. Does this mean I will lose all of my whatsapp and msn conversations? It could be a really dumb question but none of my friends knew for sure, and I would rather update the apps manually than risk losing my conversations. Thanks!