I booted up the linux machine in a rescue environment then ran this command:

fstrim /

This did not take long to complete.  Once it was done I shutdown the VM

On the Hyper-V server in powershell I then ran this command to start the compact:

Optimize-VHD C:\VM\yourvmvhd.vhdx -Mode Full

Reference:
https://www.altaro.com/hyper-v/compact-vhdx-linux-filesystem/