If you see the error:
Notice: Folder does not exist on server. The import process has failed. FID:
And it doesn't show any FID: XX (where XX is the actual id of the folder), then the issue is because you are hitting your max input var limit in PHP settings.
By Default this setting is set to 1000, you can change it to like 5000, etc.. and then you should be able to import photos again. Contact your hosting to have this limit changed.