I don't feel so. In my opinion, intent to reject can be sent in two cases:
1. A document is missing: This is covered in verification of documents stage.
2. You are unable to score required points/threshold points: In such a case, you are bound to get an intent to reject communication.
For all those, who score the required points as required by new rules/old rules, and have their stage 1 complete, I strongly feel they shall receive CSQ. It might get delayed, but ideally should get CSQ.
Thanks
Tarun.