Use Replace Selection to replace the currently selected stitches with the new selection.
Replace a Selection
Place an embroidery on the work area.
Use Box Select
(or another selection tool) to select some stitches.
Ensure that Replace Selection
is selected.
Click Box Select
and select some different stitches.
The new selection replaces your old selection.
Shortcuts
Select, Home Tab:
Keys: Alt, H, RS