How to repair this holes in secondary seal

What does the seal vendor say - they should be your best source? In my opinion, the repair can be a patch. It is well above the liquid and only needs to be vapor tight. The technique depends on the material. What is the material? It looks like Teflon. If it is Teflon this will be very hard due to the heat required and you might need to make a mechanical patch with a bolt, nut and washers. If it is a heat-sealable material or one that you can use glue on it will be easier. How was the fabric splice made? What type of secondary seal is above? Why can you not get to it from above?

Note: the fabric may get more holes as the diagonal arm closes the gap and pinches the fabric at the vertical hanger. The diagonal wrinkles suggest that the shoe may not be free to move outwards if required.