Elementary questions are fine!
Keep in mind that your web site is, ultimately, just a folder full of files, where each file is one page. So, if Everweb tries to put files in that folder with the same names as files that are already there, then yes, they’ll be replaced! The old ones will be gone, unless there’s nothing to replace them, in which case they’ll just stay there.
I’d highly recommend that you download an FTP client and use that to poke around your web site a bit. Knowing what’s in there will help you better understand what’s doing on. There’s a list of them on our wiki; one popular, decently good, and free one is Filezilla.