The disappearing outcome scores happened in one course that had only a single student in it. That's not what the max_input_vars error sounds like to me. And Bob, you're correct; they're using the assignment grading interface, not the gradebook, which reduces the chance that this is the error we're seeing.
They did find additional feedback in the Assignment tables via a SQL query. The only way we can figure out how to get that feedback into the gradebook is by adding it via the gradebook, so I'm manually copying and pasting the comments from the assignment into the gradebook. It's only 4 assignments with missing comments, about 20 students, so it's not an overwhelming amount of work. We still don't have an answer to why these comments won't save to the gradebook though, so we have no idea how to prevent it in the future.
Our current theory is that it's the same bug as MDL-35392, which doesn't have a solution yet. It does sound like other people are running into the same comment problem though.