Does anyone know if Domo MySQL supports UPSERT? Also known as Using INSERT ... ON DUPLICATE KEY UPDATE
Since you posted this in the Workbench forum, I'll talk to this from a workbench perspective first. Workbench doesn't currently support Upsert. I know this is something in the pipeline.
One thing you can do in the meantime is use a dataflow to create a recursive dataset. MySQL supports the "Replace Into" functionality that allows you to specify a primary key on a historical table and a smaller table (Such as a week or a month or more worth of data), and then insert the new records from the smaller table while updating any records that already exist in the historical table with the newly updated record based on the specified primary key.
There's a lot of Dojo topics surrounding recursive dataflows that would be useful for you to look at.
Hope this is helpful, let me know if you have additional questions.