I have double ups in my search results, how do I clear my index and start again?

It should be as simple as running rebuild_zebra.pl with the -r switch. But if this doesn’t work you can drop and recreate the zebra indexes. To do so for the biblios index.
As the user your zebra runs as (probably koha)
zebraidx -c /path/to/zebra-biblios.cfg drop biblios

For me that is
zebraidx -c /home/chris/koha-dev/etc/zebradb/zebra-biblios.cfg drop biblios

zebraidx -c /path/to/zebra-biblios.cfg commit

Then you can run rebuild_zebra.pl -b -r -v

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