Lot of missing info in this question.

Like, how data will be accessed (frequency).

This will determine your SQL storage engine type + table structure.

You can also adjust your table structure to protect against duplicate entries.

This is important, if it takes a long time to load your data. If you setup your structure to only allow unique data, then you can just upload your new data, without having to "drop" (destroy) your old data.

This can potentially speed up your data loads considerably, especially if you're using cheap/slow hosting for your database.

Likely good to give equal consideration to how data is used first + data loading.