Been using Sage Accounting for years so I would:

reverse / delete the journals.

go into the VAT returns & use the 'mark as paid' (or whatever it is) & put in the date it left the bank from your statement. 

Re-reconcile yor bank account to the last date you know it was right - it won't be right now cos of those changes but you can get it back to the balance say end June or whenever you last did it. Run the 'unreconciled bank transactions' report at the date of ast reconciliation & make sure it has nothing on it.

That should work! Bit of a faff but it's a one-off cos now you know you can match from the bank feed. 

Been using Sage Accounting for years so I would:

reverse / delete the journals.

go into the VAT returns & use the 'mark as paid' (or whatever it is) & put in the date it left the bank from your statement. 

Re-reconcile yor bank account to the last date you know it was right - it won't be right now cos of those changes but you can get it back to the balance say end June or whenever you last did it. Run the 'unreconciled bank transactions' report at the date of ast reconciliation & make sure it has nothing on it.

That should work! Bit of a faff but it's a one-off cos now you know you can match from the bank feed.