Version 2.4.3 has just hit the App Store dancefloor.
It’s working great! Thanks a lot! Now I feel silly for asking.
No need for feeling silly, just a coincidal 
Fixed, fixed, fixed! 
Coming back to this post four years on, but this same issue is currently happening to me on DTTG3.
I’ve only been using it for a few months, and this automatic replacement of the pdf I had been reading a few minutes ago with “Nothing selected” after the iPad goes to sleep and is then reopened has been occurring consistently. Is anyone else having this issue? Or is there for instance a setting that I don’t know about that needs to be toggled off?
It’s an issue for me too. Rather annoying when reading a large PDF and having to try and remember where you were and then scroll to it.
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Same here, has always happened, for last few years, any update.