Certainly no reason to prohibit conditions from being tied to encounters – with some notes:
There have been numerous discussions on Condition Lists (search for it in Talk) and the difference between them and Encounter Diagnoses. The link below is one to consider. The upshot is that if you want to say what health issue was the focus of an encounter, that’s the diagnosis. It you want to say what health issues a patient has – generally long-term – those are conditions. They interplay in a manner described in the link.
That said, a clinician could reasonably choose to mark a particular condition as something that was relevant to a particular encounter (PS I’ve built this very feature several times in other systems, and few if any clinicians have ever used it). As long as it’s optional, there’s nothing semantically or clinically wrong with offering the linkage.