It is rather obvious that you can only refresh only those listings from eBay that eBay has. eBay keeps ended / completed listings only for some time after they end. Thus, it is possible, that Wonder Lister has many ended / completed listings which eBay may have already deleted. Such listings, even if selected, won't be refreshed.
Follow these steps:
Use the menu option
Listings > Manage
This will open a new tab "Listings"
To refresh active listings, click on the folder "Active" as shown below.
All active listings will appear in the Grid.
Select all active listings in the Grid.
Click on the option "To / From eBay" > "Refresh" as shown below: