(I don't know what notes you're referring to, so can't say specifically, but a general response to what you wrote)
More or less, you don't want to try to copy a specific theme too closely (see the Timothy Parker plagiarism thing), which is why the suggestion of looking up your theme entries is generally made.
As for repeating themes, there's only so many variations of them possible, so given all the puzzles ever produced in all venues, it is inevitable that you might duplicate one in your own efforts.
For themes being "over-worked" in the definition I'm taking it to be, you generally want to try to find some variety in comparison to everything else that's been put out in the general time frame. You get a feel for this in solving a variety of puzzles. For instance, letter substitution themes (for instance A to LL in the 05/11/2018 LA Times) got rather repeated in 21x21 grids about a year or so ago, because more or less every single one was some variation upon the idea. In that sense, you tend to want to find something novel if you can.
Overall, there's nothing wrong with repeating a theme concept if you can put a new spin on it and the time isn't too close from the last one. This of course, as long as you aren't directly copying another one. But you want to try to be a bit novel in comparison to what people are doing in general too.
