If you try to set and remove more than one checkbox the following syntax works on my systems.
Start-Process msiexec -Wait -ArgumentList '/I .\check-mk-agent-2.1.0pXX-abcdef.msi WIXUI_REMOVELEGACY="1" WIXUI_CLEANINSTALL="1" WIXUI_MIGRATELEGACY=""'
If you try to set and remove more than one checkbox the following syntax works on my systems.
Start-Process msiexec -Wait -ArgumentList '/I .\check-mk-agent-2.1.0pXX-abcdef.msi WIXUI_REMOVELEGACY="1" WIXUI_CLEANINSTALL="1" WIXUI_MIGRATELEGACY=""'