I can’t remember why the undeleted field data bothered me, but I imagine it was the same as Michelle: it was showing up on the front end.
Certainly it was problematic enough that I opened a bug report.
In any case, when data is deleted but not removed from the database that feels like a bug to me.
The way that I imagine you would fix this problem is by deleting the data from wp_postmeta via AJAX when the user deleted the Flexible Content row. I imagine this would be much more efficient than trying to clean it up when the post is saved.
