Hello @corehan,
if I understand it correctly, the problem is that the count field from the raw event get overwritten by count field generated by stats command.
.. | rex "count=(?<count_orig>\d+)" |stats count by DATE,Region,managed_object,ALERT |where count_orig >100 AND ALARM="LINK-3-UPDOWN" |sort -count -ALARM
alternatively (not tested):
|stats count AS amount by DATE,Region,managed_object,ALERT |where count>100 AND ALARM="LINK-3-UPDOWN" |sort -amount -ALARM
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