deprecuation

11(6) In this section where any income is required to be applied or accumulated or set apart for application, then, for such purposes the income shall be determined without any deduction or allowance by way of depreciation or otherwise in respect of any asset, acquisition of which has been claimed as an application of income under this section in the same or any other previous year.

However Deduction of depreciation in case of a charitable / religious trust is also supported by a number of legal precedents.

Yes. You can do the revise return if you want.

However consult your Auditor and Management for their professsional advise.