Not sure. The sensible thing would be to make a copy to a newly named version first and try?
As the message indicates, you will have lost all your links to PDFs, your PDFs, terms, and groups and not sure what else. You can recreate the .enl file from the .DATA folder contents, but not the other way around.
This happened to one of our library users a couple of months ago, I tried all the tricks I knew without success. However we were able to get the library repaired by Adept Scientific’s Technical Team ( they support EndNote as main UK supplier). My user sent them his .enl file on a CDn by post, as file was too large to email, and was very please to get a repaired library with data folder set back to him in just a couple of days.
If you have the original data folder for the destroyed library file intact, you can try to fix the library in the following way:
Remove old library file (.enl file) to another folder.
Create an empty Notepad file and store it in the same folder where the data folder is located (NOT within the data folder, but at the same level)! The new file must have the same name as the old library and given the file extension .enl.
Mylibrary.enl  (if the datafolder’s name is Mylibrary.Data)
You can then open the new file in EndNote using File → Open (do not use the shortcut to the old file).
If you are lucky, the original library will now be restored if the data folder is undamaged. This work sometimes, but I have too little experience with this recovery method in real cases to promise anything.
This is a twist - usually we hear of deleted/lost .DATA folders, not a deleted/lost .enl file.  Have you contacted tech support for assistance? If the client is a bit adventurous, there are some third-party software that can un-delete deleted folder/files which might recover the .enl file but success varies by program. Another method would be to restore the hard drive but that assumes the client made a backup image of the hard drive (which included documents and a prior version of the .enl file).