When updating BlogEngine 3.x with the new updater you may run into some snags like I did. There are some improvements, yet some are ill thought out unfortunately. The first thing I ran into is that the Update process backs up your site. The problem with this is you may have a large amount of data in your media folder. The backup process cannot handle more than a few megabytes of files in this folder until it will fail with an error on the 4th step as “The directory is not empty”. If you get this error, most likely you have too much data to backup in your media folder. I had several gigabytes of video files in the folder which resulted in this error. To correct the problem, back up your media folder and remove the files from it, then proceed with the update. Once the update is completed you can put your media files back.
Also note that if you are using Chrome, once the update is complete, you may need to delete the browsing history and restart Chrome. I had to do this in order to get the Administration menu working properly.