Okay well after talking to someone else on my team we figured a way around all this. We're still using join but we don't have any missing entries. It look like this:
index=index1
| rex field=_raw "rex_field=xxx(?<rexA>\w+.\w+)%23(?<rexB>\w+)"
| dedup rexA rexB
| top limit=50 showperc=false rexB
| sort count desc
| join type=left rexB [search index=index2 source="source1"
| table rexA fieldA fieldB...
| dedup fieldA]
| table fieldA rexB fieldB...count
| search fieldA!="" | head 25
| addcoltotals labelfield=fieldA label="Top 25 Total"
We also added information from source2 to source1 to simplify things. Thanks for your help everyone!
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