Renaming a project does not also rename the wiki contents and their URLs, so that after renaming a project all wiki content is gone – due to wrong URLs. Re-renaming the project will fix the problem again.
Sorry, but I am not quite sure what the problem is. If you rename a project, you will automatically change its URL. Example:
Seems fair to me. The only thing you need to do is to rename your old Wiki start page MyProject to MyNewProject and all your Wiki will be back up.