For an integrated team to be removed from a division within Full-Time they will need to be removed from the division/cup within Whole Game System.
In Whole Game System
1. Log into https://wholegame.thefa.com/account/login
2. Click on your role
3. Click on the "Teams" tab
4. Search for the relevant team you wish to remove
5. Tick the relevant team
6. Click "Remove From Competition"
Next go to FA 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 red button 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.