There are issues with collections and books transferred to the SD card via calibre. I thought that the T1 driver in calibre had been updated and the latest version should work-around the database issue but maybe it's not incorporated yet.
Here is a post which describes why some of the issues happen:
https://www.mobileread.com/forums/sho...&postcount=317
Here is a post which recommends a solution to prevent database conflicts. I don't know if it will help your specific problem, but it's probably worth a try.
https://www.mobileread.com/forums/sho...&postcount=303