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.