As it happens I can point to a primary source that seems a fairly good indication that they did. These illustrations come from the illustrations of a manuscript (MS 78.A.15) by Hans Talhoffer, a noted fencing master of 15th century Germany, who is mainly famous for having been a dueling instructor and producing several fechtbucher that are still in existence and widely studied in HEMA circles today. From the fact that Talhoffer considered it worth making an effort to describe the proper way to fight with one, it's clear that they must have been used at least occasionally in duels.

Also, here are some previous threads about flail usage with more information. (I would like to particularly point to /u/Cereborn's photo of some 15th-16th century Korean flails in the first link, /u/wyrdj's detailed reply in the second, and /u/alfonsoelsabio's in the third. /u/g2petter in the fourth has links to several other fechtbuch illustrations showing flails, which suggests it probably wasn't some individual eccentricity on Talhoffer's part.)

I'm sorry this isn't a great answer, but it's the best I can provide with my own knowledge and resources.