The FE pedalling is probably earlier. This is evidenced by the unfinished 
asterisk, crossed out in A in the same place in which a is present in FE. It is likely that Chopin added pedal markings in this fragment first to [FC], and then, while adding them to A, he assumed that the pedal should be held longer (he also added markings in the three subsequent bars).
Compare the passage in the sources »
category imprint: Differences between sources; Corrections & alterations
issues: Corrections in A, Deletions in A
notation: Pedalling