I guess there isn't going to be a 100% proven answer, so I'm more interested in what possibility is most likely. In the answer on A Scanner Darkly's IMDB page to the question of whom Arctor slept with, the most likely possibility is suggested to be that he slept with Connie, and the brief appearance of Donna in Connie's place was just a hallucination.
What troubles me about this explanation is that Arctor sees the same Connie/Donna transformation when he is playing back the surveillance tapes in the police station. He plays and rewinds a hologram of the surveillance several times and still notices the same effect.
His hallucinations generally seemed to be random and brief, so I find it unlikely that he could have had the exact same hallucination both while: (a) lying in bed with Connie/Donna, and (b) reviewing the surveillance tapes. Adding to (b), he didn't just see the transformation once while reviewing the surveillance tapes - the transformation coordinated precisely with his playing and rewinding of them. It's not impossible for a hallucination to be that sophisticated, but it seems unlikely to me.
Of course, if the Connie/Donna transformation wasn't a hallucination, this begs the question of what actually was going on. All I can think of would be that:
Audrey (who goes by the name of "Hank" while in the scramble suit and who poses as Donna) was wearing some high-tech Connie disguise that briefly glitched while she was lying in bed with Bruce (who goes by the name of "Fred" while in the scramble suit and who poses as Arctor). The glitch was responsible for the transformation, and this would explain why Bruce saw the transformation both while lying in bed with Connie/Audrey and while reviewing the surveillance tapes. But then... why would Audrey sleep with Bruce? She seems very concerned about Bruce's well-being when she drops him off at New-Path and later talks with Mike about him (Mike is another undercover agent who poses as a New-Path employee), but why sleep with him? Did she feel so bad for him that she would sleep with him? Or, was she in love with him?