Each yer I have to get the books checked by the accountant and then an auditor. During that period I will update new membership payments (some 150-200) into my existing version. Once the auditor returns his audited version of the Manager system is there a way to merge the audited version back into my current version. Last year I just imported the QIF file into the auditor reconciled version. Took me some 20 hours of work.
It depends on what your accountant will change. The only way I see is through batch update or create but I see it very error prone. You should better get a server/cloud edition in my opinion.
Generally by Journal Entry.
If you have a printed copy of the BS and P&L before you send the files to the Accountant / Auditor, then get a printed copy after their review, take up the details of any variances via Journal Entry using your Financial Year End date.
However, unless your account keeping is particularly sloppy, I what expect there would be very little variation. Should take you less than 10 minutes if they have provided you with the details.
Once you understand their variations you can make the required adjustments prior to the next year end, so that there is minimal or zero adjustments.
I am not sure that I would allow anybody, accountant / auditor, to make direct entries into the main accounting files without the business first knowing what the entries were about.
The accountant / auditor are only reviewing the accounts, not maintaining the accounts.
Besides, they have to many disclaimer clauses which they can rely on to protect their rear ends.