Yeah, I've had a lot of issues with the flood alert, and the times I've set are a bit generous here. Honestly, I'd consider trying
gsync instead. It doesn't suffer from the the flood alert since it's not writing anything. The bottleneck would probably be how fast you can upload to a remote server, which should be pretty quick.
Granted, I have not tried it with a large number of small files, so it may need some adjustments (e.g. raising max loop limit).