I'm assuming that the duplicate transactions aren't tagged to any invoices since they are duplicates?
You can roll back a VAT return, but they need to be done in order (newest first). This will only roll it back in QuickFile and doesn't affect your submission to HMRC. Once it's rolled back, any locks will be removed for you to make changes.
You will need to re-submit your return on QuickFile (again, this doesn't affect HMRC and in fact, they will reject it as a duplicate). It's important to check your figures however. If they have changed, you may need to notify HMRC. I would suspect they won't change. As per my first paragraph - if they are untagged, they're unlikely to have any bearing on your figures.
I hope that makes sense? If in doubt however, as @manish suggested, check with your accountant (I'm not one).