Andrew

Andrew Hi, you can run trim operations using the fstrim tool. You just need to be sure you mounted first the volume before trimming

sudo fstrim -v /path/to/the/mounted/volumeor 

Also, you can use sudo fstrim -Av or sudo fstrim -av to trim all mounted volumes

And that command is listed in the doc linked for you......
https://kaosx.us/docs/flatpak/#managing-applications