Thank you for making a bug report.
I’m not sure where you have your YGO omega installed, but I’d hazard to guess that it doesn’t have permission to manage the files where it is installed. I have tested the ability to delete the deck and it works fine.
We can follow up here, or you can get faster help by reaching out on the Duelist Unite Discord server in the #omega_help channel.
I found the solution by running the .exe as administrator, thanks to your guess that it might involved not having permission.
My problem might also be caused by installing the game in other directory, not the default path. Maybe, if i installed it in the default path, this will never happen. I will leave it here for suggestion, in case other people get into the same problem as me.