Here's my beef. In Vyrso, you have this competitively priced book that you can search in Logos and have simple references linked.
And then it gets LOGOS-ed. 
Suddenly, it gets pulled from the Vyrso. Now, all of a sudden you have to pay twice as much for it. That's if you're lucky. If you're unlucky, it gets tossed into a bundle of a dozen other books, so that you have to order all of them to get the one you want.
For what? What was wrong with it in Vyrso? Oh, now it's linked better with your resources. But I don't care if it's linked better, I just want to read it! Too bad. 
Let the Nations Be Glad was priced at $10.19. Now it's gone from Vyrso. You can get it in Logos Pre-Pub though, but with 19 other books, for a grand total of $269.95! And who knows how long it will take for the whole bundle to get through Pre-Pub.
Will the Logos version be superior? The Scripture references will be checked, and the footnotes will link to other books, but at best that will save you a few seconds of pulling up another resource in the library. And some Logos resources are still poorly tagged.
Here's my plea -- if you publish a Bible Commentary, or a Bible Dictionary, or some other reference work that's made to be linked to Logos features, have it be a Logos resource.
But if you publish a book that's meant to be read through... keep it in Vyrso. I'd much rather have it competitively priced than have it priced twice as high and/or put into a bundle just for additional tagging.