The limitation that you are describing in your post. If I’m not misunderstanding, you are splitting the book up chapter by chapter, rather than just importing the whole thing and allowing LingQ to split as it sees fit. You are then doing something to split up your audio file (it’s not clear the source of the file, but regardless). It sounds like you are hoping LingQ would have a solution to all of this, although it’s not clear what you are asking for exactly. All of these sound like “limitations” to what you are attempting to do.
So my point is simply that, LingQ has not done anything to solve any of the limitations that I think you are implying in the 8 years I’ve been using them. It’s not likely that they will change any of the current behavior. So my suggestion is simply to import the e-book as is. Read in LingQ doing all the look ups you normally would using LingQ, while listening to the audio separately from LingQ (via audible, or mp3 player, or whatever your source is). You can pause the audio as needed if you need to look something up.
You’d be spending more time learning than fiddling with individual chapter splitting which sounds like it is taking up a good portion of time.
The last book I imported actually did split up by chapter automatically surprisingly (although longer chapters were split up additionally). I haven’t tried another since, so I don’t know if I got “lucky”, but in the end it doesn’t matter all that much in my opinion.
Anyway…just a suggestion.