If you go to the bank account record there is a tick box to have no bank reconciliation on the account, you can untick it after clearing the audit trail.
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Yes you need to deal with the VAT reconciliation, it appears that you have backdated unreconciled transactions in your accounts, this is not uncommon, normally we include these in the VAT return at the next run as we go, typically these are late entered purchases which we want to claim the VAT back on.
If you are really unlucky then you could have back dated sales and a VAT liability, if this is the case you need to rectify it on the next return to avoid the penalties. Should you have a VAT inspection before you rectify it you should declare it at the outset so as to not get penalties on it.
If you know the period and you know why the return was not reconciled then you could do a dummy return to account for the vat and not submit it. You will need to keep copious documentation to explain this to HMRC should you get asked.
I have encountered some serious misunderstandings about how to do the VAT return including people who ran if for the date range and never reconciled the VAT return. These can be an absolute nightmare to fix and to get to grips with.
I would be inclined to run a VAT return to the end of the last period and include the unreconciled transactions to see what has been missed and most importantly answer the question of why those transactions did not go on previous returns. If you have made historical mistakes then you need to rectify them on the next return. It could be that these are purchase transactions you have never claimed and you have a substantial VAT refund due, you need to run it and find out.
You need to proceed with caution here, if you make a mistake that is in your favour and not in the favour of HMRC, it could be considered tax evasion and you could face serious personal consequences. You must understand why those transactions had not gone on VAT returns in the past. You must have an explanation of why on every vat return since you did not include them (as Sage will prompt you at every run to include them).
Hopefully it is not a serious issue, and the amounts involved are small.
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