1. Yes.
2. You can mark them as Complete or just Delete them.
3. Yes, there will still be entries in some of the database tables. That shouldn't cause any problems. If a user tries to grab a data file that was referenced in one of the runs, it will be reported as not available on disk. If users want to clean up the list, they can just delete the runs through the standard UI. Note that this is completely separate from deleting the files on disk.

Thanks,
Josh