I’m experiencing the exact same bug as Track has no opacity? - #3 by daniel47, in Shotcut 25.9.12. (That post claims it was fixed in 22.06.23) Translucent clips suddenly have black backgrounds instead of showing the clip underneath them, and my tracks have no blend mode option in Properties. As suggested by that thread, I created a new track and it does have a blend mode option and blends properly.
I am using 25.9.12 installed via apt on Debian forky. The problem started occurring after not touching the project for a while, so it’s hard to pinpoint a proximate cause, though it may have been because of an update.
This is your problem. We did not release a 25.9.12 version and build the software you are using. Either use something from our download page, or ask whoever made your Debian package for help.
It appears that the upstream version is 25.08.16, and there are no patches. Is the “version” that Shotcut reports just the date it was built?
I have confirmed the issue persists with the AppImage build shotcut-linux-x86_64-250816.AppImage.
I think you misunderstand the fix in the other thread. It seems to fix the bug that makes something incorrect in the project, but it does not fix an affected project. You can upload your project file here for someone to try to reproduce it and/or manually repair it for you.