It’s probably the limitation of solr, which is database used to store the index.
You can use variant embeded in YaCy or standalone one.
Last time, I tried to solve this, I ended in reading docs about solr clusters – then there should be no problem with limits. But since I had a workaround (in my case it was not index itself, but database of links, so I switched to non-solr), I didn’t try the cluster solution.