Late registration of vat

My wife runs a ice cream shop,I’m now looking at her books,she clearly has gone over the vat registration 93k,I’m at a loss as to what to do,do we have to pay the vat on all 93k or is it over the amount of registration 83k(this for year 16/17.)
We have subsequently gone over this season..
Do I just register now.
What can I expect to happen.
Meeting my accountant next week,but,would like to have an idea of what course of action is best,
This wasn’t done as avoidance,I work away,she just banks all the money and paid the bills.
The business is seasonal,April to October,she closed this year in September because we went over.
Any help would be. Appreciated,.