When you do Bulk Exalate on a trigger in GitHub and you have more than 1000 issues, not all issues are synchronized.
It seems there is no indication that your search has hit this limit - there is no exception or error.
Due to the limitation of the GitHub API, the search is limited to 1000 issues.
This is a known issue on GitHub.
It affects the Bulk Exalate operation if there are more than 1000 items fitting the search query you use to synchronize issues.
Modify the search query to select a subset of issues. For example, you can add a date parameter to the query.