Yes, I would recommend deleting the newly received tokens if Koinly is treating them as the same thing (which it usually does).
Koinly will report the errors if your balances do not match the reported balances. You can choose whether to continue and generate your reports or if you would like to fix the errors first.
We would of course recommend that you import your data as accurately as possible but Koinly will take the conservative approach and assume a cost-basis of $0 for any asset that has an unknown origin. This makes it so that the reports can be used even if there are missing purchases but your gains will be higher.
Also keep in mind that there is no limitation on the number of reports that you can generate with your tax plan. If something is wrong on the report or if you need to amend your transactions then you can jsut generate a new report
Best regards,
Petur