You will need to make sure that you have fully disconnected the old account to do this go to Reports > HMRC view the account and then click the disconnect button
I’d start over, i.e. first disconnect all accounts from that page to completely empty the table, and only then connect again. When you connect make sure you selected organisation rather than individual, and if you have several gateway accounts make sure you’re connecting the right one (to be 100% sure actively click the sign out link on https://tax.service.gov.uk/business-account before you start the connect process from QuickFile).
Then go to reports -> VAT returns -> settings, and make sure you’ve got the online filing and MTD boxes both ticked and your HMRC account selected in the drop down, and that your VAT number is correct.