If you see this alert when you open ProPresenter 6, it means that you have added files or folders to your Library folder that should not be there. This generally happens when you have added your media folders to the ProPresenter 6 folder in the Documents directory, but it could really be any file that doesn't end in *.pro6.
This is an example of what the folder structure could look like that would cause this alert message to appear. As you can see, there are song files and the media repository folders. The folders are what triggered the alert in this case. It could also happen if someone accidentally dropped a file into the folder in Finder without realizing it.
When you click OK on this alert, a new folder called Invalid ProPresenter Documents will be created on the Desktop, and every file that isn't a ProPresenter document will be moved to that folder. Depending on the cause of this alert, this may or may not solve the issue for you.
To verify this issue won't continue to happen, open ProPresenter's Preferences and take a look at the General settings. In the example above, the file path for the Media Repository has been set to the same directory as the Library files. If nothing is changed in ProPresenter in this instance, any new media added to ProPresenter is likely to cause this issue to immediately occur again if Managed Media is enabled. You can see in the image below that the path for the Library and Media Repository are the same. (Keep in mind that ~/ is the same as Users/CurrentUser/. To resolve this issue, click on Custom Path and select a new location, or select For All Users or Only this User to change the path to one of the default locations. Check that Support Files hasn't been changed to a Custom Path in the same location as well.
Once you have changed the path, you may need to relink ProPresenter to the moved files, especially if it was your Media Repository. The easiest thing to do is to rename the folder called Invalid ProPresenter Documents to something a bit more descriptive, then place it somewhere that is safer than your Desktop (and not in your Library folder). Once you've moved the folder, you can change the Custom Path to that newly moved folder. Just click on Custom Path to relink. You'll be able to navigate through a Finder window to select the correct folder.
After you have relinked to the folder, restart ProPresenter. All of your media files should now relink and the alert should be gone.