If my customer's payment goes through but the ticket does not get issued, does my portal still hold the booking?

Yes, the booking is not simply lost. Taking the payment and issuing the ticket are two separate steps, and when the second one fails the portal keeps the booking in a pending or failed ticketing state instead of throwing it away. It stays visible in your admin panel with the passenger details, the flight and the payment against it, so nothing has to be typed again from scratch.

From there you normally have two ways out. You can try issuing again, which often works if the failure was a brief problem at the supplier's end rather than a fare that has gone. If the fare has genuinely disappeared, you either rebook the customer on what is available now and settle the difference with them, or you cancel and refund the payment you have already taken.

The honest part is that neither outcome is guaranteed by the portal alone. Whether a retry succeeds depends on the airline and the supplier, and on whether that fare still exists at that moment, which can be minutes rather than hours. How quickly a refund reaches the customer depends on your payment provider and their card issuer, not on your portal, so a customer who sees the money leave their account may wait a while before it comes back.

The practical habit is to look at the pending and failed ticketing list in your admin panel at the start of every day, and to call the customer yourself before they call you, because a booking sitting in that state overnight is the one that turns into a complaint.