The first version of 'Fantaisie en ut' was composed in 1856. We know it was played by Franck in Paris at Cavaillé-Coll's workshop on a newly built organ which was meant for the cathedral of Carcassonne (in southern France). This 4 manuals organ had two enclosed divisions: a "Grand Récit" with foundations and reeds 16' 8' 4', and a much smaller "Petit Récit". Franck wrote carefully on his score the registration for this organ.
But for some reason, the organ was eventually shipped to Luçon (western France) without the "Grand Récit".
Later, in 1862/63, Franck composed another "Fantaisie en ut", with three entirely new parts (perhaps for the inauguration of St-Sulpice?)
The "Fantaisie" op. 16 published in the "Six Pièces" in 1868 is a mix of these two versions: it has the beginning "Quasi lento" of 1856 version and the middle and ending parts (Allegretto cantando, Quasi lento, Adagio) of 1863 version.
In 1868, Franck wrote a 4th version for the inauguration of Cavaillé-Coll organ in Notre-Dame, Paris. This 4th version was beautifully recorded by Aarnoud and uploaded on this site under the name 'Fantaisie pour Notre-Dame': https://www.contrebombarde.com/concerthall/music/42775
Score on IMSLP (with a few mistakes): https://imslp.org/wiki/File:PMLP121161-franck-fantaisie-v1.pdf