Some of our customers are facing issue when all Scheduled Issues are turned inactive.

We have investigated this case with Atlassian (and one of our customers): 

The root cause in summary was the exact same time of execution of many issues, it was firing 403 error (licence missing), while it was a timeout issue, but as our app gets response from Jira about missing license, the SI's were deactivated.

As a solution:

Please try to spread creation of sets of your issues by 1 minute eg. in 5-10 minute window.

Additionally:

Please vote for this ticket in Atlassian support system, as it related to issue and will help to fix it: 

https://jira.atlassian.com/browse/JRACLOUD-71056