If you delete the pages from the server, but not from the local host, then yes, if you do a complete synchronize, the pages will be re uploaded to the server.
Deleting the content [pages should not have any effect on the CMS Admin, they are desperate entities. You can have content in the CMS that does not have a physical page to display on.
if you are hesitant to delete the files, then just back them up to another location, you should be doing this as a matter of course anyway.