Can my manager ask me to be in at 9am if I have a flexi hours contract?

I work for a local government and have two children. I’ve worked in my current role for four years. My contract states that I’m entitled to flexi hours as per the council’s contract. However, when I first joined the team my manager informed me that they needed staff in the office from 9am to 5pm. I never disputed this. However, due to childcare issues I have been coming in to the office after 9am, usually between 9.10 and 9.20am. I’ve been doing this for around three years now with no problem and make up my hours and much more. Recently in supervision my manager raised timekeeping with me and said I must be in at 9am. I explained that due to childcare (taking the kids to school) I’m unable to come in for 9am, but my manager stated that this is the time I must come in and on the off chance I’m late I must ring in. My flexi working allows me to start between 8am – 10am, to take lunch between 12pm to 2pm and to leave between 4pm to 7pm. I can also take off two flexi days per month. Although I’ve not used flexi my manager’s boss stated we could use flexi. My manager’s boss starts at 9.30 due to childcare. My question is can my manager ask me to come in at 9am even though I have childcare issues and the office is covered by another colleague. Also why wasn’t I given the option to change my hours say 9.15 to 5.15pm as this is what I’ve been doing?