When you have a Jira flow filter in place with issuekey, if the issue key(s) in flow filter are deleted from Jira, this may stop sync from working.
Example Flow Filter: status='Open' AND issuekey IN ('XYZ-1','XYZ-2')
If the issue XYZ-1 is deleted from Jira
You will see below kind of errors in the log.
3.x
This is because the JQL still tried to fetch/get the records based key in flow filter and since it could not find the key, Jira does not return any record and sync wont work.
Remove the issuekey from the flow filter for it to work.
Updated Flow Filter: status='Open' AND issuekey IN ('XYZ-2')