First of all - make sure you ignore the advice to update your software … since this is now unsupported and supposedly discontinued - I would not trust intuit one iota not to completely break the workaround using system date …

second - I had the same issue and used Anna money to bridge my return .

To reconcile VAT in QB - I used the option in the file VAT to make a return under the £85,000 threshold , just ignore the warnings and there might have been an option to do a paper return … or similar. 
I can’t remember exactly 

Anyway - worked fine !