In conventional CAN frames stuff bits are added from the Start of Frame (SOF) through the end of the checksum (CRC). After every five identical bits a complementary bit is inserted. These stuff bits are not calculated into the checksum.
With CAN FD the stuff bits are also added right after the SOF. However, this rule now ends with the data field. The transmitting node calculates the checksum by including the stuff bits that have been added to the frame. A stuff bit counter (modulo 8) and a parity bit are next in the frame.
The CRC field itself is stuffed also, but with a higher frequency. Here the following rule applies: The CRC field always starts with a stuff bit complementary to its predecessor. After each four bits which follow, whether they are identical or not, a stuff bit is inserted complementary to its predecessor.
After the CRC no stuff bits are inserted any more as is the case in conventional CAN.