Cleaning devices and operations for downhole separation in a well

A system comprising:

• a downhole separation system to be positioned downhole in a multi-bore well in a subsurface formation, wherein the downhole separation system is configured to receive formation fluid from the subsurface formation and configured to separate formation fluid into a production fluid and a nonproduction fluid, the downhole separation system comprising:
• at least one filtering device to be positioned in an opening of a downhole tubular, wherein the at least one filtering device is to filter out at least a portion of solids in at least one of the formation fluid, the production fluid, or the nonproduction fluid, to prevent the portion of solids from entering the downhole tubular;
• a controller configured to initiate an operation to clean the at least one filtering device using a cleaning fluid, a production fluid pump to pump the production fluid for delivery to a surface of the multi-bore well;
• and
• a nonproduction fluid pump to pump the nonproduction fluid into a second bore of the multi-bore well for disposal into the subsurface formation comprising a downhole disposal location surrounding the second bore.