I had this exact same problem today! You would think simply pressing “Cancel” would work, but that just caused the program to freeze faster.
I used a pretty simple work-around. First, close EndNote. Then, go to the folder that you told EndNote to autoimport from, and rename the folder (or move it). Now open EndNote again. You’ll get an error message that EndNote can’t find the file to import from, but after you press “Okay”, you’ll be able to use the program again. I suggest going to your preferences and either disabling the autoimport, or maybe setting up a different folder for autoimport, one that has only a subset of files (my file had a LOT of pdf’s in it, so I’m thinking that’s what caused the error, but I’m not sure).
I hope that works for you! Good luck.