Apart from the obvious solutions that you quoted (splitting into smaller files containing one or two events is definitely more appropriate), could you first check this: does Fosstrak partly store the events that come from a same single file?
You can check the epcis-repository.log on the Tomcat’s log directory to see if the timeout is due to a long processing time, and query your repository after the timeout capture to check how many events where stored –if any.
HTTP Post capture is synchronous, which is not the best way to process big files. Alternatives may require developing an asynchronous protocol (like the ones proposed in EPCIS standard) or a front-end that would split big files into single events before processing the capture.
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