This should be fine. Here's what I would do, find a subset of the data on a test MA process that has a few records in that table. Delete all of them that relate to that test MA process and make sure the UI loads fine. If that works you know you are ok to remove the rest.
Also this might help you https://www.mcbeev.com/Blog/February-2015/Ensure-Your-Kentico-EMS-Site-Is-Running-At-Peak-Performance