Currently, the automation rule updates a maximum of 100 objects for Scheduled trigger in a single run or Branch on AQL as documented here: Jira Automation Branches

Suggestion:

• Remove the limit from the update count per scheduled run.
• User should be able to update all the relevant objects in a single scheduled run instead of running the automation rule multiple times if the object count is more than 100

Workaround:

• Increase the scheduled interval for the automation rule so that it can update all the required objects in multiple runs.
• Alternatively, make use of Dynamic Looping.