The airline will have record of her booking and boardings.

Advise the airlines that the original boarding passes were not retained, and request credit despite it.

It may be helpful to try to help the airline help you by referencing the PNR/record locator/confirmation code of her booking.

If, for whatever reason, the airline declines or otherwise hems-and-haws about it being the "passenger's responsibility to ensure travel documents are appropriately retained, etc.," keep pressing.

This can be done, and has been done many times by many others not limited to myself. It's really not that big of a deal.

Good luck.