Thanks for the report. Unfortunately I can't find anything in the log that indicates that CC deleted the book file. With one rare exception, CC logs whenever it deletes a book file. I have added logging for that exception. I have also added a check to the "read book" function to verify that the book is actually there just before it launches the reader app.
The log does show that metadata for that book was downloaded during 4 autoconnects. The file was still there after the first 3, so it seems that autoconnect isn't the culprit.
This leaves us with the question: how did the file get deleted? The only suggestion I can make is that the SD card file system might be damaged. Does your phone support being mounted as a disk (by a cable) on your computer? If so, you should be able to run a disk check on the SD card. If not, do you have a card reader attached to your computer? If so then you can use that to check the disk.
Is there any sequence of taps in your reader app that could delete a book file? Given that the book is on an SD card I suspect the answer is no.
Is it possible that something like ES file explorer ran and "cleaned up"?
I know I am clutching at straws.
I hope that if it happens again then the extra logging I have added will help find what is happening.
Regarding the problems with sorting after running find missing books: the intention was that a sort in missing books get redone when going back to the book list. Clearly it wasn't happening. I fixed that.