Chopra, who already ensured his PGA Tour card for 2014, had rounds of 72 and 69 on first two days and is lying tied 43rd, a fall of 19 places from his overnight position.
The lead is shared by Americans John Peterson (71-68-67) and Andrew Svobda (72-65-69) at 10-under 206. Three others -- Troy Matteson, Peter Mainati and Greg Owen -- are tied for third at 207.
The Chiquita Classic is the second of the series of four tournaments in the newly established Web.Com Finals.