When you have available credit from HMRC, this will not automatically apply to the following period. That's the reason that the negative VAT Return doesn't carry over to the next filling.
I suggest adjusting your VAT return before you submit it to HMRC. This way, you're able to enter the adjustment amount for available credit and it will carry over to the current period. Please note that any manual adjustments you make to your return will impact your VAT control. If you are not sure about making an adjustment, I recommend consulting an accountant to help you guide in making an adjustment so your account stays accurate.
Here's how to adjust:
Click Taxes at the left panel. Then, select VAT and select Prepare Return.
Click Adjust in the VAT line that you want to change.
Choose an Adjustment Date and VAT rate.
Select the Adjustment Account drop-down menu and choose an account.
To change the adjustment because you received credit and you owe less VAT to the government, select an income account that you create for this purpose.
If you are making the adjustment to include a fine, penalty, or interest on a VAT return, select an expense account, such as Interest Expense or Non-deductible Penalties.
In the Amount section, enter the amount of the adjustment. Then, enter a memo to describe the adjustment.