If you have availability syncing enabled on your listings, Host Tools is your "parent calendar." This means that Host Tools will only pull actual reservations from each of your connected channels (Airbnb, VRBO, etc).
Host Tools will not recognize any blocked days from those calendars and will open them back up. Any dates you want blocked need to be blocked directly on the Host Tools calendar.
Here are the steps to blocking dates on your calendar.
Click and drag across dates on the pricing calendar as you would to manually add a reservation.
Click on the "switch" next to "availability override" to change the dates from available to blocked.