R1 and T4 issues

My spouse's head office is in Quebec but he doesn't work or live there. He gets an R1 and a T4. He has over paid CPP and EI premiums and paid into QPIP. The software has dealt with the QPIP payments by adding them to the EI over payments but it isn't doing anything for CPP and the summary says he hasn't contributed. How do I fix this? Are there forms that I should be manually editing like the Schedule 8 or the RC381? Any advice would be appreciated!