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Could it be the vibration of the HDDs? If you say a re seat fixes it they might come a bit loose. Maybe try using some tape or hot glue to hold them in place?
To add to this, could also be a cold or cracked solder joint making intermittent connection.
If you get desperate, you can look at reflow options. I know the old Xboxs people would bake. Best to just take a look at the solder joints for all the connectors. Are they still shiny? Or dull and cracked?