As of 1.5.3+, database enrolment updates are done on user login. If the user doesn't login, the enrolment information is not updated.
Starting 1.6 (under development, not even Beta), there is an external script that syncs Moodle and your external database, as often as you like (you have to run it externally).
Saludos. Iñaki.
Enrolment
External Database Update Interval
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