The issue appears to be real. Sometimes reindexing helps, in other cases not. There are now about 1M results in Google for lost email following an El Cap upgrade. That is not a trivial number. If I go looking for something that turns out to be an obscure problem, the result count is at least an order of magnitude lower.
I've had the good fortune of only needing to deal with a Mail problem once, but that thing is the worst POS compared to any other mail client out there. Once it starts down the "won't cooperate" road, good luck.