If there are no programs defined, the SQL at line 179 of enrol/programs/classes/local/calendar.php fetches all calendar events, not just those with a component=='enrol_programs' as both "LEFT JOIN"s just produce null values. I think the "AND e.component=..." in the first "LEFT JOIN" isn't doing what you think it is.
As a result, the following code then deletes every event.
This is from the moodle version 4 stable branch of your code.

This is run at 1 minute past every hour as a scheduled task, so you don't have long to create a program before all your calendar events are wiped.