From your description I would guess that the input sources of those 4 channels were changed. With a RML32AI as slave I think they should be set as network inputs, but there is also some interaction between master and slave, so you always have to watch both sides...
Otherwise there is only one thing you can try is a full factory reset with option card unplugged. The "how to" is explained in the documents you can find in your Presonus account. A factory reset sets ANYTHING back to zero, which sometimes helps to make things work again. It is the "ultimate" tool for you as user, but of course it can not repair defects. It just makes clear that there must be a physical defect. As you have backups of your scenes you will not lose any information, so give your board this "refresh"! If a factory reset does not help, send the board to service. Open a service ticket in your PreSonus account.