Here's what I would do. I'll talk about a few possible methods of doing so.
If there was a character who was not affected, I would try to make him make sarcastic remarks. Like "Its not like I haven't heard that a million times already", for it to be kept subtle, it could be something that people in general usually ask the character about. Like a piece of gum for example.
He/she could then leave more blatant clues over time, saying more obvious things. Like predicting exactly what the characters are going to say, knowing EVERYTHING about them (because some time later in the timeline, this character was told about these important details due to an increase of trust or whatever), etc.
If you want it to be a mystery, you could have numerous other elements. "Red herrings" if you want to call them that. You could make up urban legends. Like something mystical that could be the cause of the timeline "resetting" but really isn't. Or better yet, have a different urban legend throughout each timeline (I think the trick might be to make it..."fit in" so that it isn't jarring or too obvious). In this way, you could decide which ones are real/fake/working together and so on.
Jeez. You're the one writing this story, yet I'm trying to build your world for you.
As for how to make your story interesting....well a person's interest is always subjective so you'll mainly have to hope they try to read your story.
However, here's a tip. It probably helps to learn how to structure your story. You could learn the three-act structure but I (when I feel that I can correctly execute the ideas I have with my own webcomic) would probably use the Larry Brooks method.
Here's an overview:
Its summed up as: Hook, Set-up, First Plot Point, Response, Midpoint, Attack, Pre-Second Plot Point lull, Second Plot Point, Resolution
The "Hook" is that intriguing event that hooks the readers to your work. A good hook (to me) makes the audience want to keep reading your series to see how things got there/how this thing will come into play/etc.
A good hook I can think of is Persona 5.
(Stop at the 14:45 mark for spoilers past the hook)
The hook successfully...
Introduces the protagonist
Shows us the main opposing forces
Show us some intriguing elements (like the beasts he fought and what he's being accused of)
Obviously you don't have to have your protagonist in your hooking scene (since its mainly used to garner interest, set up something intriguing/mysterious, etc.). But this the latest example I have, also I really like Persona 5. There are many other ways to achieve this.
Another thing, use your calendar on the story. As in set actual dates.
To make your plot interesting (or to gather interest), I would try to hint at the nature of the "timeline shift" all the way at the Set-up. I would also make sure to make good introductions for the characters you created, build up the setting, characterize the characters, all of that stuff. Its important to focus the conflict on one of two things.
1: The Timeline
- Something that the characters have to deal with.
For the first choice, I would structure the setup so that the event you mentioned is about to happen. When it does happen, I suppose you could put them back on the timeline. Also remember when I said "use the calendar"? Make sure not to tell them the date, but put it in the background somewhere. Also, whatever the characters did before this event, I would try to make a character (the one I talked about earlier) reference something that they did together in this other timeline, but have nobody remember it.
It might also help if the character is generally the....third wheel if that makes sense. Like if he's put off to the side. Make it SEEM like the characters would do that but then make that not the case.
Continue with this, until someone realizes "this happened before hasn't it?". You then reach the first plot point and now you are on the response.
- For this, I would basically make the conflict more personal to one of the characters. And its worth pointing out that this conflict would have to take place MUCH earlier than "the event" you mentioned. You basically do the same structure (of course you have to shake things up, to not make things predictable) as #1. Jeez, I wrote a lot already but you probably get the idea.
Anyway, as for your calendar for #2? The moment the conflict ends, have that conveniently line up with "the event". Then when the timeline reset happens, make it seem like a new day. Like you know those days where you can't believe something happened, like if it was all just a dream?
Make it like that, except nobody (or almost nobody) remembers what happened. Heck, I would go the extra mile, just to screw with the audience. Like, with every previous chapter you wrote, I would update every chapter title with something saying "Outdated" or "Discarded" and not explain why this was done until the very end of the story.
Now not everything I wrote is the "book of storytelling" or whatever. Its just advice. It was also me rambling. I urge you to do your own research, check out the link I provided for Larry's method of story structure (as well as check out his website, Storyfix.com and look at the three-act structure). You can take this advice or leave it, I have a lot of work to do on my storytelling (and art) myself.
On a side note, I probably talked for way too long. Most of this should have been your job but I just butted in, my bad.
Anyway, good luck with your story. Hope this helped.