You may notice that after getting rep all your rules are gone, well, worry not, you can get your rules back!
All you need to do is the following:
1- Start repentance
2- Get into the game with Da Rules on
3- Close repentance
4- Head to "Documents\My Games\Binding of Isaac Afterbirth+ Mods/da rules_2403871374"
5- Copy the files named Save1.dat and the other SaveX.dat that may exist(one for each slot).
6- Go to the game's folder
---6.1- On steam, right click the Isaac game on your Library
---6.2- Select Properties
---6.3- Go to Local Files
---6.4- Click the "Browse..." button
7- Now, on the games folder, go to "data/da rules/"
8- Paste the save.dat files from step 5 and replace.
9- You are Done!