I found a CPA before I was told I was being audited and we planned to file an amended return because as I suspected the original accountant did everything all wrong.

@Dave SaveriHe may need to issue an amended 1099-MISC with $0 showing on the form.He would then need to issue you a 1099-INTIn turn you will need to issue a 1098 to him if it is secured by real estate.

I'd amend your least with a clause stating that after 30 days, the rent goes up by $xxx.

I don't see this being amended anytime soon, but hopefully it's in the mid term/long term road map! 

I can't see how this benefits anyone.You should suck it up, apologize to the tenant for the misunderstanding, ask her to stay and send her a lease amendment approving the dog. 

(2) If I didn't claim depreciation, do I file an amendment or a catch up?

@Steven Hamilton II hence the reference to the TPR applicability...I've requested an amendment to the BP article.

I have asked an attorney but haven't heard yet from him.Is it too late to amend the contract as you suggest?

If you didn't, you'll need to go back and amend your 2010 return.You'll use your basis in 2010 (including recaptured depreciation) and compare it to market value in 2015 when it was placed back in service and use the lower of cost or market to value the property.  

Can't the contract be amended during my option period to state that I would like the property to be vacant by the date of closing?