The limit is generally set to 1000, but if you try to go over that, you get an immediate error, not a timeout.
How many issues are you exporting, how long do you get before it times out, and does the log file say anything about the export?
There are a number of different settings that you should look at. I would look into the Database timeout settings first. Then into any JIRA timeouts that you can set.
If you are behind an web server proxy they have timeouts as well.
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