The only edition I own of Fantasie Op 49 is Paderewski. In the critical notes the editors wrote:
Bars 112 and 116: Although the original french edition, Breitkopf and even Mikulli's have the octave E flat - E flat in the bass in the beginning of these bars, we accepted the change introduced by recent editions by analogy to bars 279 and 283. It's obvious that only the extension of the keyboard obliged Chopin to modify the most adequate version.
(the translation is mine, my edition is not the English one, sorry for the inaccuracies).
At least in the time the Pad. Edition was published, the Chopin's autograph of this work was unavailable. Also, by the time Fantasie was written, the lower key available was C in the bass. Probably the last piano Chopin owned reached the A but, as I know, there are no known late hour corrections of the works made by Chopin in the cases that they could benefice from the wider keyboard extension.
So here comes one eternal dilemma for the piano performer: to use or not to use the wider extension of our keyboards in the works composed in a shorter keyboard. We must guess if the use of the wider extension would be approved or if it was even intended by the composer but frustrated by the actual extension of it.
(My personal opinion is that the B flat works harmonically better and has a greater musical and aesthetic effect. I think that Chopin intended to write it but he wrote E flat instead due to the lack of lower notes on the piano he owned while composed this and another works).