Sorry, no. If you’re implementing key pinning in your app, I recommend (a) you use the standard HPKP techniques, and (b) you follow the HPKP best practices described here.
If you’re pinning based on the hash of SubjectPublicKeyInfo, as HPKP does, you shouldn’t have any problem, since the SubjectPublicKeyInfo stayed the same. But it sounds from your message as if you are pinning based on the hash of the whole intermediate certificate.