Hi, thank you for your detailed feedback.
Regarding the issue where Video Upscaler AI shows that all files in the queue have been completed, but only some files are actually exported and some files are processed twice, we have confirmed that this issue has been fixed in the latest version 4.1.1.1.
Please download and install the latest version 4.1.1.1, then try processing the batch again.
If you still encounter a similar issue after updating, please feel free to let us know in this thread and provide the related log files and screenshots, so we can further check it for you.
Thank you again for your support and patience.