If you are referring to an estoppel certificate for the benefit of a 3rd party, such as a prospective purchaser of the property, the certificate is used for you to state truthfully (so that the purchaser can rely on your disclosures) the terms and circumstances of your tenancy. It is usually prepared by the landlord for you to sign. It does not modify the terms of the lease although it may require you to affirm that a particular use is not being made of the property. If so, and if you are using the premises contrary to the representation in the certificate, you should insist on striking that provision or you should not sign the certificate because it would be untrue.
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Based on your description and comments, you need to take your lease and the estoppel and any other documents to a local landlord tenant or real estate lawyer for a consultation.