For reimbursing the management fee,

You can delete the payment (if it is auto-closed) in the management fee invoice for that period and then update the management fee amount.

After doing that, log payment > update the payout amount using the refresh icon in the payout line item and then pay the owner.

Please refer to these articles for more the steps:
How to update management fee?
How to refresh the amount due to match the report data?