Related Questions:
What happens when authorized payment is captured from the stripe dashboard ?
Can we capture payments on Stripe dashboard and send updates to Chargebee ?
Why cannot be the payments directly captured at Stripe dashboard?
Why should auto_capture parameter be set to manual while creating intent via stripe JS?
Clarification:
When a payment capture request is initiated from Chargebee , an entry is made at Chargebee end.Once the payment is completed at Stripe gateway, Chargebee will receive event notification via configured webhooks with transaction reference and corresponding status will be updated at Chargebee end.
In case when payment capture request is not initiated from Chargebee there is no reference about the transaction belonging to which subscription/customer etc. So even though web hooks are received due to corresponding mapping issue details will not be available in Chargebee.
Note : If you still want to capture payment at Stripe end, you need to manually log the transaction on the Chargebee dashboard.