It can be amended anytime, if both partners agree..

Since the 1031 is the purchaser of the property I always think it is good to disclose that up front most intermediaries have language they want you to put in the contract about the seller cooperating with the exchange at no additional cost to them.You could do an amendment later, but what if for some reason they refuse to sign or can't sign.I'd say avoid the surprises and unknowns with this and just get it done up front.I suppose you might loose some of your negotiating power as they know you have a time crunch to spend your money, but that could be the case anyway when you pop the amendment on the seller too, if not disclosed up front.

Certain amendments and clauses? 

Someone with more familiarity of the law or an attorney may correct me.1: If provisions prohibiting leasing were in effect before the owner bought, and before Jan 1 2012, they are applicable2: Starting Jan 1 2012 no provisions or amendments can be made prohibiting leasing for greater than 30 days regardless if it was made before/after owner bought in community3.

I would amend your lease agreements going forward to include a specific time that a tenant needs to be out on the last day (5:00pm mountain time, for example). 

I hope you'll amend your contract to have a dollar limit on expenditures that can occur without your authorization.

My options were to file and amend the return when i get K1's vs not filing and applying for extension until Oct.Based on my current tax situation I was actually receiving a fairly substantial refund from the IRS and my CPA he has recommended we file return and then amend the return when we get the new K1's as opposed to file an extension since I'm being offered a refund from the IRS.

Is there a way to amend the lease to be a contract with the LLC after the fact?

If not I suspect the first thing the debtor needs to do is file an amended plan that describes the terms of the proposed sale and notice is provided to the creditors to give then the opportunity to object. 

There have been significant amendments since that time.