For an integrated team to be removed from a division within Full-Time they will need to be removed from the division/cup within the competition portal (You can see how to do this by clicking here)
Once the team has been removed from the division, sign in to Full-Time.
In FA Full-Time
1. Login to https://fulltime-admin.thefa.com/gen/Login.do
2. Go to Setup > Teams
3. Go to the relevant division you wish to remove from team
4. They should show as "inactive" and a link saying "Remove Fixtures" should be displayed, click this button whereby you will be given the option whether you want to keep/remove fixtures and results
5. Finally click "Edit" where you can select "Hide from standings" if necessary.
