All private keys can be recovered from the 12 word pass phrase, so nothing can be lost, it’s explained in Counterwallet FAQs.
Counterwallet Helper script can work with an very large number of addresses (10,000 has been successfully tested) to recover all the private keys. Can you create more (say, up to 20) new addresses in your Counterwallet?
If that doesn’t help, use Counterwallet Helper to list more on your own PC.