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)
run
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

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

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

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