There are two parts to the audit regime. Firstly, an internal auditor, appointed by the parish council, will undertake an audit of the finances, policies and procedures. The internal auditor reports their findings to the parish council and completes one part of the AGAR, the Annual Governance and Accountability Return. The AGAR is then submitted for review to the external auditor, appointed (indirectly) by the Department for Communities and Local Government. Smaller authorities meeting certain requirements may exempt themselves from the external review by completing a declaration of eligibility. If you Google the Local Audit & Accountability Act 2014, you'll get a better idea of how the process works.
The issues you have raised should have been picked up and reported by the internal auditor. If the missing invoices relate to regular or known suppliers, you could ask them to provide duplicates. On modern computerised accounting systems, this is usually straightforward. Did you have a Clerk/RFO at the time the documents were processed? If so, can you ask that person why they are missing? Do you think that this is just incompetence, or do you have reason to believe that rules might have been broken? You should certainly ask your internal auditor to comment on the issue, as this will help you to decide whether or not you have the right person undertaking this important role.
If the sums of money are small and there is no evidence of misfeasance, it's probably best to draw a line under it and start again, following standard procedures from this point onwards.