If you have prelates surrounding the Catheral carrying relics and put them in the catheral at the same time. all the relics will go in and the bonus apply to all of them
I actually believe this is true for all buildings where you can store relics
still no bug fix for this @SavageEmpire566 , please add this to known issue, many people have reported this yet no response.
They already responded to you in the other thread you made. Reignitz Cathedral can store more than 3 relics - #5 by SavageEmpire566