If the same document may be relevant to multiple timelines, you probably need to do a bit more thinking and planning — although I suspect you can come up with workable solutions.
You might consider duplicating documents that have multiple timeline dates, although that doesn’t seem terribly attractive to me. Remember that, if you change the creation or modification date of a replicant, you change all instances of that document.
You might use tags to designate timelines; that may have potential. Any document can have as many tags as you wish.
I have no idea how many documents you may have, or what you mean by a ‘timeline’ date (is it a specific YYYYMMDD date, or a historical period such as 13th century, or some other reference such as Bronze Age, or even combinations?).
I would avoid getting into a system that involved enormous drudgery in exhaustively tagging or marking thousands of documents, as you could spend endless hours on the mechanics without getting more productive work done. Unless, of course, the project is to exhaustively catalog and organize a collection of references — which is the kind of project I personally avoid. 
I would look into the possibility that, instead of organizing each and every document in multiple ways, I could create rich text notes to accomplish similar objectives for some important concepts. For example, I can, on the fly, Option-Command-drag into a rich text note multiple items from a search list or smart group. I might be interested in only a representative set of items for such a list, not the entire list. In that note I’ve collected some important references as clickable links. If you’ve used the trick of modifying creation dates, you can run a sort in a search list by creation date and select any desired range of dates, for example. Remember that, for a major reference document you might create several notes with different topics and/or timelines.
Your question about marking items in a smart group in some way so that you can identify new content that hasn’t been tagged or marked in some way gets tricky, especially if you are using a mark like a Label color, and some of the content in one smart group is going to be present in multiple smart groups or search result lists (I tend to use a Label as a temporary mark and erase such marks when an action has been done). One thing to think about is making a note of the ‘Date Added’ when you last worked on the content of a smart group, as that will help you immediately identify and sort by that property so as to work on newly added content.