After re-reading, realized that response didn't really answer the question ... so ... am sticking my neck out cause I don't run windows, but ... on the linux platform, I've never found a 'graceful' way of ending a process. kill -9 pid does the job, but if the process was involved in building a backup, the process never reached the part in code that 'cleaned up', thus manual clean up was necessary, unless there is a scheduled clean up. 2.7 now has scheduled task that one could run manually but didn't see in the listing of task the clean up of moodledata/temp/backup/ files and diretories (folders). There is one to clean up backup tables, however.
If you haven't implemented auto backups yet, then sounds like one is anticipating issues. The first run autobackups will be perhaps the most intensive. There is no info in the tables that Moodle could use as to when the courses were backed up last, etc..
There is a way to kinda tippytoe into auto backups, however. Install course size report. Run it. Get the course ID's of the top 5 courses in size .... let's say it shows 5,234,65,31,and 1014.
Use the backup.php script in moodlecode/admin/cli/. that script takes two parameters ... course ID and the destination for the backups.
In one shell script (I've heard Windows now has "powershell" so you might be able to use that), create the backup command for each course on a separate line:
php /moodlecode/admin/cli/backup.php --courseid=5 --destination=C:\whereever
php /moodlecode/admin/cli/backup.php --courseid=234 --destination=C:\whereever
php /moodlecode/admin/cli/backup.php --courseid=65 --destination=C:\whereever
php /moodlecode/admin/cli/backup.php --courseid=31 --destination=C:\whereever
php /moodlecode/admin/cli/backup.php --courseid=1014 --destination=C:\whereever
Once the script is created, pull out a timer, and start your timer the same time you start the script.
You'll get a better idea of how long the largest courses will take.
Thus, might be able to make a more educated guess as to the scheduling of automated backups in the Moodle UI - would think non-prime time for users in courses - wee hours of AM ... say 2-4 AM.
It's been years since have been in Windows and I assume one can cancel execution of such with keyboard strokes [ctrl][c]. To see what will happen (find out what will be needed to clean up) run the above script and during the first course backup try to cancel it. Then go check moodledata/backup/temp/ and see what's there. Also check the systems C:\temp or C:\tmp directories.
That command line script would only involve PHP executing queries and then executing some action to build backup files, as well as talking to MySQL (eventually) to update tables related to status of last backup, date of last backup, etc.. Killing the script shouldn't affect persons in Moodle using. Remember, there is a scheduled task that cleans up DB so one might not need to do anything DB wise.
'spirit of sharing', Ken