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Unfortunately I think you have discovered a bug, JS. I’m not sure we ever tested the batch output file with so many hydrographs. This is something we will log and address as part of our next build, but it will be some time (several months I suspect) before we release the next version.
In the meantime, you can at least get the results from the individual run output files. The other workaround would be to create two catchment files, which are the same except for the number of print locations. If you keep these to less than 250 in each catchment file, you could then run the model twice and generate two batch output files which combined contain all the peaks.