you need to build missing faces ( with networks )

copy paste the 2 circles ( to trim later )

I delete the two faces with circles ... select the four borders ( don't forget to join the segments of each border ) and apply Planar ( to prevent possible gaps )

join the 6 faces of the piece ( it says Solid ... good for booleans

paste + trim the circles and the flat faces ( then you can delete the round disks )

and loft between the two circles

finally copy all faces included the round surface ( the loft ) and paste elsewhere ... then join to have a solid

( I work on the half piece and do a mirror + boolean union )

3dm file joined

Thanks, this is helpful. I will try to repro the repair steps, and keep things as object in my workflow.