Approving an exception to a contractual requirement, such as a specified deadline, essentially means that your organization is choosing not to enforce (or “waiving”) the particular requirement. It is generally not necessary to have both parties sign an amendment to the agreement every time a requirement is waived, but it may be advisable to do so if the exception is something that could repeat or impact other obligations.

Indemnification language in a contract is traditionally understood to apply only to third party claims and not to “direct” claims between the parties themselves. Many courts will presume this interpretation unless the parties clearly express an intent for indemnification to apply to direct claims. However, courts differ on this issue, so it is important to clearly state that indemnification only applies to third party claims if that is the interpretation your organization wants.

The purpose of “entire agreement” language in a contract (sometimes called an “integration” or “merger” clause), like the example you mentioned, is to avoid misunderstandings and disputes about terms that may have been discussed during negotiations but were never included in the final agreement. When drafted properly such a provision should generally prevent one party from seeking enforcement of promises outside of the written terms of the contract.

Executing a contract in counterparts is a very common practice that simply means that each party signs their own separate duplicate copy of the agreement rather than signing together on the same page of the same document.