Two possible solutions, depending on what has happened.
If they are all opening as Acrobat files because somehow you changed the extension from .EML to .PDF, then re-naming them back to .EML should solve the problem. There is a way of doing this as a 'batch' process but I have never used it so cannot advise, but you could google 'batch rename files' and see what you get. Try it with say four or five before you try it on all of them !
The other possibility is that you have merely changed the 'association' of the file - this is what determines what application is the default for opening it. Again, this is easy to change.
Open Windows Explorer and find one of these files, then RIGHT click on it You will get a small menu with about half way down 'Open with . . .' Click on 'Open with' and a list of the programs associated with the file will appear. At the bottom of this list you will see 'Choose default program', click on this. Then the 'Set default' box will open.
If your e-mail program is listed, merely select it and make sure the box at the bottom left 'Always use . . ' is ticked. If your program isn't listed, click 'Browse' (bottom right) and go looking for the program you want to use. Once you have found it, select it and then make sure the 'Always use' box is ticked.
If neither of these work, post back.