You will have problems. Though we do generally use relative urls, relative urls are always relative to the root of the site not relative to the virtual directory. So for example all of your friendly urls in the mp_FriendlyUrls table will map to real urls like
whereas in a root level site it would just map to
There will also be broken image urls in the content.
It would have been much easier if your dev environment matched the target deployment environment.
Hope it helps,