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We could be able solve this issue by setting 32 MB limit for uploaded files download and will be working on optimizing it. I suggest you to use date ranges and search to narrow down submission counts per download.
I will update here as soon as there is an update about this.
Please let me know if you need further assistance.
Downloaded zip is now limited to about 250 MB with maximum 250 files inside. So in your case, it will be better to have around 100 submission in each date-range.
Thank you very much for your patience.
All the best