Clearly I have no knowledge of your particular circumstances but given that we are now at 30th September, when external auditors must complete their audit so that appropriate conclusion of audit notices can be published on websites and notice boards for town and parish councils, I'd say that things are not always as they may seem. Maybe you need to clarify the situation with your current (and I assume) new clerk.
Firstly, clerks around the country are bemoaning the fact that despite having documentation since May onwards, external auditors may not have completed their work yet. It's a perennial issue that the industry needs to address but as a rule, external auditors will try to justify not completing their work and must produce an interim statement that can be published by close of business today. The reason their work hasn't been completed I'm not going to guess but sheer volume of work coupled with possibly inexperienced students being used (as many clerks will suggest) can lead to queries being raised by the EA which may be justified or sometimes not. Are the auditors "refusing" to complete or are they saying they've not had a response or a response they deem adequate? Auditors generally don't "refuse". They may issue a qualified report if they're unhappy with what they've found; they don't and, I'd suggest can't, "refuse".
When your interim clerk said that things were well, he/she may well have assumed that to be the case at the time. Unless you ask, you are simply guessing. For my own council, the AGAR and supporting papers were sent off in early May but it was only last week that we had our conclusion of audit notice with no queries raised. If a query was raised I can't help thinking it would not be concluded by now.
Before blaming anyone (auditor or clerk), I'd check the facts.