You can create another entity with same attributes to upload Excel data temporarily. (do the excel configuration accordingly)
In microflow, fetch data from the actual database(where data will be saved finally) using retrieve activity.
Use loop activity and inside activity retrieve single data from newly created entity using xpath for the unique key so that we will get the same record
Then do the comparison using decision activity and then update the data or if its new record create the record. And commit the list.
Hope this helps!