I would use an existing file instead of creating a new file for a new Dorico document without erasing instruments in Setup mode.
However, Dorico always loads all instruments, even the instruments which are not allocated to any flow.
Is there a way to prevent this?
Why not set playback template to silence? Then no instruments will load.
OK, thanks. But…
What should I do if I want to load two instruments which are used in flows?
You could leave the playback template set to HSSE or whatever your default is, unassign all instruments in Play mode, save, then manually reassign as needed.