Hey Ben.  So cool that you bear the name of an ancestor born in the 1700s.
  
I think I can answer a couple of your questions.
First, yes, those pages that are in the National Archives have been removed from the bible.  However, when they were removed, the information was re-recorded.  Comparing the handwriting on all four pages you can see different penmen.  I have some thoughts about this but its speculation.  I do not believe old Benjamin (1769) kept the record himself because the info we have on him suggests he was unable to write.  I think the second record was probably made by his son Andrew using the original as his source.
As to the whereabouts of the bible today.  I believe I have located it.  I spoke to a woman who inherited it but does not want to be named.  It is in family hands in Spartanburg County, SC.