Splitting an already signed document

Our business is small and we work with a lot of contracts.  The contracts contain multiple documents in one large document for signature.  The concern is that after the client signs the large document, would we be able to pull out the smaller documents and save separately? An alternative if the files could be linked together in some way so that they were still separate but there was one smooth signing process versus having to open all the separate documents to sign them.

For example, we send an Offer Package which contains the LOA, LOE and MA (master agreement); all three smaller documents (LOA,LOE,MA) must be separated for the purposes of providing to our funder.

Thanks.