Fortunately, we have all the raw records and can still get to them.
Unfortunately, there's only one person doing this (sherm) and he's overworked now... he used to handle a few payment issues per day, now he's doing tons.
We talked to another site that uses PayPal in the same way we do and they're also experiencing problems, so it's not our problem. PayPal has yet to get back to us (grrr) so we're just hoping things will get resolved in time.
In the meantime, be patient while sherm manually enters your payments.