The concept is that if no one ever suspects a mystery, then the discrepancies never become clues. The intention at the end of the episode is to create a façade that will appease them enough to avoid investigating. Clearly, if they investigate, then they will ultimately find evidence to again reveal the truth. Altering their biological clocks, for example, is probably not something even they can do, & maybe a transporter trace analysis focused specifically on that might reveal that fact again, but if no one ever thinks they need to run one, then they won't be looking for it
The episode doesn't hinge on eliminating all the contrary evidence. It hinges on eliminating the mystery that they become compelled to solve.
At the start, Data talks about realigning their clock with the nearest starbase. That takes care of any time discrepancy, unless they go rooting through the computer's recesses, to look specifically for the chronometer tampering, which Geordi later finds
The whole mystery unfolds with Beverly's stupid plants. If not for that, they may never have even bothered to look deeper. I assume it was a minor fix, that. Data's fake sensor image was enough to get them through the initial curiosity, & it only falls apart upon closer attention, & there won't be any paid if they don't suspect it. Plus, they might have chosen a less obvious image the 2nd time
Worf's arm only becomes a clue because he's specifically ordered to report oddities. Without that, he's unlikely to come forward, by his own admission, & if it ever did come out in the future that he'd broken his arm & had it refused, he'd likely assume it happened at some other time. Plus, Beverly probably gave him some pain suppressants so he wouldn't notice it.
Data's odd behavior only becomes odd when put under scrutiny & he's forced to tell unsupportable lies. Nobody's beards grew. They removed them just like normal. The soil samples weren't the issue. The plant growth was, & just like the beards, they could be corrected easily enough, most likely by replacing all the plants with appropriate ones
The only X factor in this episode is Troi. Her emotional & psychological reactions to having been possessed are unknowable by us, but since her whole alien empathic thing is a bunch of sci-fi gobbledygook anyhow, then it's not much of a leap to suggest they figured their way around it. After all, it only really surfaced when Picard made them all reflect on the event. Apart from a little initial disorientation, she seemed fairly functional until then. You've got to suspend some disbelief on that one. It's fricking Star Trek. Maybe the aliens did some extra special memory wiping on her so she'd be ok the 2nd time
I like the episode. It's one of my S4 favorites
