Tshuvot HaRaShbA vol. VI was published in Warsaw 1898 (not 1868 as in the imprint- RSZ Havlin, introduction to Tshuvot HaRaShbA, 2000 p. 25), long after the publications of the previous volumes. Consequently, much of the material in this volume is parallel to responsa that had already been published. The publishers had the integrity to retain the order of the manuscript, and merely cited the parallel source where previously published responsa appear, alongside the respective number of the response in the manuscript.
With these features, it would be expected that we could easily identify the manuscript source, once it came up.
Hannan Benayhu, who now manages the manuscript collection of his father R. Meir Benayhu z"l, graciously allowed us to photograph two of the most important items of this collection, that we have had no image or record of until now- the Talmud Yerushalmi fragment from Sanhedrin VI-VII (shelfmark Sp 12), and the 167 page manuscript of Tshuvot HaraShbA (O 204).
The latter is clearly the source of vol. VI, bearing the following features of identification:
The marginalia on the first and last pages of the manuscript, comments by, respectively, David Pifano and Binyamin Qimhi, were retained in the published edition.
Responsa that were omitted in the edition appear in the manuscript here with scratchmarks, presumably an indication to the printer where to omit. In the margins of these responsa, are pencil-written references citing where the specific response has been published.