I haven't heard of a problem like yours. I do know a couple of people have had issues with different micro SD cards. Some of the issues have been fixed by formatting the card with
https://www.sdcard.org/downloads/formatter_4/. There have also been issues with different cards that have been fixed in firmware updates.
Where does the device stop? Showing the boot screen or somewhere else? The rest, is that just a pinhole reset, or a factory reset?
What happens if you insert the card while it is running? With 3000 books on the card it will take a while to process the card, but it should come up after awhile. There are two stages. The first shows nothing on the screen, but the device information screen will show the card. You can continue using the device, but if you try connecting to a PC, you don't get the "connect" prompt. The seconds stage is the black processing screen as the books are added to the internal database.
Also, what happens if you just put a few books on the card? I know you want the full library, but if there is an issue, testing with a lot less books should help to sort things out.