You should have backups. I mean, considering that 500GB external HDDs costs dirt cheap, compared to what it used to be, I think everyone should have a external HDD for Time Machine backups. The drive is going to fail eventually. Plus, if you want to retrieve a deleted file, you can easily do that by entering Time Machine.
The answer to your question is, no, it will not. Your data will be kept. Remember that an upgrade from Leopard to Snow Leopard kept all the data on your HDD? Same here with Snow Leopard to Lion.