From Cubase 9 manual:
https://steinberg.help/cubase_pro_artist/v9/en/cubase_nuendo/topics/project_handling/project_handling_removing_unused_audio_files_t.html
- Select File > Cleanup.
However, the option “Cleanup” doesn’t exist, and I was unable to find this section in the Cubase 11 manual (A link to change versions between manuals could have been nice)
Anyone knows how do I do that in Cubase 11?
I just go to pool-select unissued files and then move to trash.
This is not the same action. The manual section I attached claims to be cleaning unused audio files from Cubase project from the entire storage of the computer, your solution is for a specific project only.
If you empty the trash it clears it from the computer too surely. That’s what a trash can does.
Let me rephrase that - the action described in the manual claims to clear unused files for EVERY project in the computer. You action does that only for that specific project.
The Clean Up function were abondoned after Cubase 9… I have C9 installed for this feature alone… And Yes, it works for all Cubase projects/songs also made with the newer versions (a Cubase project file is a cubase project file).
Why they got rid of this is way beyond me. It was the best way to clean up/delete files NOT tied to any Cubase project/song.
This function was espesially useful if you saved multiple versions of the same project… As it is now, and you delete things with the Empty Trash function you have NO indication if that file is used in an earlier or other version of a Cubase project… and you might erase files you need in other projects.
If you only remove your files from the pool and or trash can (without erasing), you may be left with a bunch of unused files all over your audio disk…
So to you who have use for the Clean Up function, keep Cubase 9 installed on your computer… Then you can open C9 and use the Clean Up function as you used to… That’s my workaround for a brilliant Cubase feature left behind.
You are absolutely correct… Read my other post for a workaround 
Thank you for your answer!
So what you’re saying is that I need to install Cubase 9 to use this feature? The download manager allows me to install versions as old as 9.5, is it available there or is it only in 9.0?
Ah I see yes. That is useful
Cubase 9.0 is the last version to include the Clean Up feature. It is NOT in Cubase 9.5… So you have to get hold of the installer for Cubase 9.0 (the last update was 9.0.40).
How to I get an installer for Cubase 9.0?
You may try to contact Steinberg support, and explain your reason for getting hold of a Cubase 9.0 installer.
It’s on their download page