Your accountant will need to provide a detailed letter explaining he discrepancy. If he is unable to do so, I am afraid that this may adversely affect your application for ILR.
As it currently stands, there is no further extensions to Tier 1 permissible.
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If you have any further questions, please do not hesitate to ask.
Your accountant should explain how he has reached the figures he has reached and what this consists of. He should also also provide a copy of the information used to reach the calculations.
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You will have to submit a fresh application and your accountant will need to supply the information as stated above.
If it is refused, you should have the right to appeal in country.