As Richard has explained, when you had your assets as "do not transcode," you should have left them alone. with the exception that they might fill the disk up, but none of the errors you have had point to that.
Although normally, you'd set the project format to a3c audio, and the wav files would show "untranscoded."
You should always run Encore "as administrator." It may have nothing to do with the errors you are seeing, but it invites odd problems. Just run as administrator and take that off the table.
The specific error you are getting has most often been due to filename length. Max is 80 characters including spaces. I can't imagine after the troubleshooting you've done that they are this long, but who knows! Yes, special characters etc can be a problem. I don't recall the issue, but I would also look at file path length/depth.
Look also for gaps in any of the Premiere sequences.
> Free space in my C driver (now I have 27GB of free space, I guess it's enought for Encore to work, right ?
No. Temporary files/caches/transcoded files can quickly swell things. Do you have a separate drive for the video files, etc?