Informal/pre-existing flexitime/banked hours scheme

some of the team have been running a flexi-time/banked hours scheme without their current manager knowing. It was approved by a former manager over 3 years ago and not communicated during handover. The team are never asked to work over and above their hours but chose to do so and then bank their hours for a Friday pm for example.

We have a separate TOIL policy and if they are asked to do an event in an evening or weekend, then they can claim Toil.  This is followed by the whole business, but the flexitime scheme is used by 3 members of staff, the current manager doesn't sign off flexi-time and it is not one of our policies.

The manager now wants to stop the scheme as there is no business need for it, would custom and practice come into this as a former manager informally agreed it.  There is no written approval.

If so, I presume we would need to consult (the contracts give the right to change terms).