Choices are:
Wait for the mfg to re-package, no guarantee when that will happen.
This is the long term solution. Are you a big enough customer for them to
care?
There may be a price increase due to the change.

Use as is and rework as necessary. The potential early mortality escapes
are a concern.
There is a cost for the rework and you may or not be responsible for infant
mortality based on contract.

Bake the parts.
Known cost (from your description non trivial) and known results.
It is a PIA.

Decline the contract to deliver additional units.
Hurts the relationship with the customer whether internal or external.

Any other alternatives?