Fitness of gnucash for professional audit

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Our business (a small private school) uses GnuCash for our accounting.
 None of us are accountants, and recently we decided to hire a CPA to
give us an audit so we can apply for a business loan.  (We are a 501c3
non profit).  We were unable to find any CPAs who had even heard of
GnuCash.  My understanding is the GnuCash is a suitable QuickBooks
replacement and that a CPA should be able to navigate it just fine.
However, I am wondering if the CPA will be able to see all our
information in a format familiar for for them to do their work (just
outputting reports, not exporting to a non-free program like
QuickBooks).  Does anyone have any pointers that I can pass along to
the CPA as he tries to produce financial reports suitable for a bank's
review in a loan application and for auditing our accounting system?
If necessary, is there an acceptable way to convert from GnuCash to
QuickBooks or Quicken file formats? (I've googled it, I'm just asking
about people's experiences here.)

Within our business, we use python scripts to output reports that make
sense for our internal understanding of our finances.  We have our
"checking account" subdivided into official budget categories and
unofficial working categories (such as money set aside from the
official budget to specific purposes), some of which are a couple
levels deep (ie: checking account::educational resources::Art
supplies).  Any observations, links, advice or pointers based on your
businesses experience would be helpful.

Thanks,
Elliot