Excellent questions:  Recording was a new and novel device, unknown in both early England and the colonies, and only after recording statutes were passed in the mid- to late 18th Century could a land transfer be sworn to before other than the judge of general jurisdiction for the county.

Thus, deeds were drawn and acknowledged during "court days", and though there were JPs and other judges who were permitted to accept oathes/affirmations, deeds were excluded from their jurisdiction.  So, the vast majority of such documents were acknowledged by the parties in open court, following which the Court directed that those were to be entered of record by the clerk to the court.

Only after those recording statutes came into play did we have registers/registrars of deeds as we have now.

Who owns those deeds left at the courthouse has been questioned a thousand times, I suppose.  The unwritten answer is that all documentary materials left - abandoned - with the clerks of a courthouse become the property of the county, and may be disposed of in the normal course of the county business.   

I have not see what you describe as "...many cases of old original deeds still in the court houses that were never fully proven...."  While I am sure that such do exist, I would wonder that there are "many".       

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