There is much written about this family and links to Thomas Paine; further research may be helpful to you.
Some records indicate that:
Thomas Paine's manuscripts passed by bequest to Madame Bonneville (mother of Benjamin Bonneville). This lady, after Paine's death, published a fragment of Paine's third part of "The Age of Reason," but it was afterwards found that she had erased passages that might offend the orthodox. Madame Bonneville returned to her husband in Paris, and the French "Biographical Dictionary" states that in 1829 she, as the depositary of Paine's papers, began "editing" his life. This, which could only have been the autobiography, was never published. She had become a Roman Catholic. On returning (1833) to America, where her son, General Bonneville, also a Catholic, was in military service, she had personal as well as religious reasons for suppressing the memoirs. She might naturally have feared the revival of an old scandal concerning her relations with Paine. The same motives may have prevented her son from publishing Paine's memoirs and manuscripts. Madame Bonneville died at the house of the General, in St. Louis. A note from his widow, Mrs. Sue Bonneville, says: "The papers you speak of regarding Thomas Paine are all destroyed -- at least all which the General had in his possession. On his leaving St. Louis for an indefinite time all his effects -- a handsome library and valuable papers included were stored away, and during his absence the storehouse burned down, and all that the General stored away were burned."