I am not sure that Cli is able to extract more than 1000 issues.
The only way I know is to change 1000 to another value in a property file of Jira.
I haven't seen any issue with that change for many months...
Here are some JIRACLI Examples for 3.8.0 (https://bobswift.atlassian.net/wiki/display/JCLI/3.8.0+-+Examples)
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