As students get enrolled in the course, that shouldn't impact your gradebook, but I can understand the hesitancy! Also so you don't have to do this over and over again for each student...
Since you are importing grades, you should be all good to re-import as much as you need without duplicates occuring. The grade import process will just override whatever is already in the gradebook and replace it with what is in the spreadsheet. If something is not in the spreadsheet you are importing in but is in the gradebook already, Canvas won't mess with it.
A small aside- because the import process will replace existing gradebook values with ones in the spreadsheet (if they exist), it's important to keep in mind that if a student has redone work and gotten a higher score or something along those lines, when you import the spreadsheet, that would be replaced with the value from the old gradebook. So just keep an eye out for that!