This hard limit is set to 3,000 because having more than that has shown to crash browsers even on the most powerful machines.
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We do realize that for some use-cases this is an issue, and we recommend for now to just create multiple sitemaps of specific sections of the website.
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However, we have future plans to offer much higher limits, once we are able to replace the D3 technology currently used to visualize the map, with a more scalable solution. ( not an simple task )