Pandoc -f html -t native shows that <br> is turned into a Linebreak element:

pandoc -f html -t native
test <br/>
[ Plain [ Str "test" , LineBreak ] ]

So I'd use a filter that converts Linebreaks to Space. Save as removeLinebreak.lua:

function Linebreak (elem)

  return pandoc.Space()

end

Could be added to the previous one with

}}

I think replacing it with a space is the safest. To remove it entirely, you couldn't return nil as Pandoc treats this as "leave unmodified". You'd have to return an empty list instead, I think: