I was aware of the skipping of non modified courses and forgot to mention we have about 1000 additional hidden courses in addition to the 500 active courses, we keep the previous years worth of courses on hand for quick access. Of the 500 active courses there may be 100-400 used daily. My moodledata folder is about 260gb, I'm guessing 1/3 or less of that is actively used.
I guess there's only one way to estimate how long this may take, try it out on our development server (much slower than production) and if it is mildly successful try it one night in production and monitor results.
I was wondering if anyone had some real life examples for automated backup duration times. Does anyone think 500 courses in 6hr in the middle of the night is not realistic? If it takes longer than 6hr would that be a red flag of something wrong with our system? Would it be more realistic to budget for 1min/ea course backup rather than 45sec (most course backups <50mb), maybe budgeting for 8hr is safer?