Generally I would advise NOT to do such things. There's not a good, or rather, not annoying, way of doing so.
I've seen a few people mention timers or hidden embedded links and both of those seem difficult to implement and, more importantly, annoying, prompting players to wait on every single page for an arbitrary amount of time just in case there's a hidden time condition that could be met (which they of course want to meet in order to achieve the best play through), or in the case of embedded links, clicking on every word with the fear that if they don't they'll miss the best outcome for the scenario.
Likewise, you'd have to mention to the player that these elements are a thing because otherwise they'll have no idea to expect them, given how strange and rare features they are, and that takes away from suprise and causes the previously mentioned behaviours.
It's like hidden walls in dark souls. Once you find one, you just got to go punching ALL the walls, JUST IN CASE you missed some super OP BS behind some wall, only your situation is way worse due to a lack of visual cues you can give players.
I'd say just write your story assuming that the reader is invested. Obviously give them a hook at the start and give them a goal and a reason to be invested and all that, but don't assume you're audience isn't invested in you're writing (ie don't assume they're just skimming your work) halfway or at the end of your work.
If the reader wants to "charge blindly through" your work, either a) they personally don't car enough to read everything (time constraints, repeat reading, wanting to just post a comment, god forbid they enjoy speed-reading/skimming) in which case implementing features like that will only slow them to a crawl and serves as a deterrent more than a reward or b) your writing isn't engaging them, which you can't fix with gimmicks, only better writing.
Alternatively, the people who are going to spot that stuff we're probs paying attention anyway and didn't need some gimmicks to entice them to do so, so it's a wasted effort.
Just focus on rewarding your readers' attention to detail by having them recall past information to overcome challenges (ie recalling the elemental weakness of an enemy and using the appropriate attack) whilst also offering something less effective for those who didn't pick up the finer details or aren't able to spot them/ don't want to go backtracking (ie Using inefficient attacks and expending more resources as a result) whilst still allowing progression (I hate game over screens in CYOA...). Choice of Games generally uses stats as a reward, so you could try something like that (ie picking the appropriate response gives charisma). I rather enjoy such things, AND they allow you to test the skill of the player and their knowledge of the game (The Lost Heir's hidden mastery classes are an awesome example of this).
tl;dr 1) Reward attention through scenarios where recalling information given previously allows the player to gain a gameplay advantage, 2) focus on strong writing rather than weird gimmicks, and 3) believe your audience will show an appropriate level of investment and attention if you've given them a reason to do so, and if you can't give them a reason, then improve your writing.
Btw, in the case of a secret passage, give them the ability to pick multiple actions, eg: In the grand master's quarters:
a) Remove the blue book from the bookshelf
b) Pet the cat
c) Jump on the table
d) ect....
Establish in a previous chapter that the grand master loves cats, and then if the player picks the cat, boom, secret passage revealed. If not, game continues as normal.
EDIT: End mentioned "Contradictory information". The application of that could work in the same way, so that's something else to consider.END EDIT
Obviously they can just "go back" and keep trying, but again, that's a limitation of Chooseyourstory and not something that can be changed. You have to trust in the audience to see their story through. Something that can go a long way to this is not making the secret passage the 100% objectively better choice. Have another, less optimal award down the other path (ie Secret tunnel gives sword, normal way gives potion of healing). Basically don't give them just one optimal path, b/c that path will then be abused on repeat playthroughs and a whole part of your story (the non-secret passage way of progress) will be ignored. EDIT: What I mean here is that a sword and a potion can both be useful, but a sword is more appealing and useful during maybe initial playthroughs when your reader doesn't fully understand intricacies of the game mechanics/story.END EDIT
GL with your story, and remember: First and foremost, it's a story, not a game. EDIT: Focus on writing, then gameplay, and I'd recomend not having a True End. Embrace a CYOA medium! END EDIT