You’ll never be able to get them. I’m in the same situation as the OP and you for favourites; I got about 18 pages worth and the same number as you, then nothing.
The reason the pages don’t always return 200 tweets is because, as per the docs, deleted and unavailable tweets are removed after they’ve been queried. So, if you’ve deleted 10 of your last 200 tweets, when you try and load 200, you’ll get 190. Clearly the index is still kept somewhere and still counts towards the initial 200 total.
I imagine it’s the same with favourites, so I can only guess the link to that tweet being a favourite is still stored somewhere and once you’ve favourited it, even if you un-favourite it, it’ll still get removed from the results. This makes sense; if you have followed someone for ages, unfollow them, and follow them again, you don’t appear at the top of their followers list, you appear way down the list where you were before; clearly that link is still kept somewhere, and it must be the same with favourites, i.e once the link is made, it’s only marked as ‘inactive’ if you then undo it.
I created a topic here Tweet index limits about the limits, because the 3,200 limit has been present for years, way back to when the Fail Whale was a daily occurrence; Twitter’s infrastructure has come a long way since then but unfortunately these API limits are still imposed.
I think the official response from Twitter, if one was ever given, would be “tough, this is how it is”.
¯_(ツ)_/¯