I realized today that I'm having this same issue. The text in the email shows 1.4 million total alerts. I realize it should only give me 500,000 of those, according to the support article. But when I open the .csv in Excel, it only shows 50,001 rows like yours. It shouldn't be related to the .csv file size, because the email is only 386KB in size. This is on LEM version 6.3.1hotfix1.
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