[stumped]

More info would help:
what format are the lost books and where did you get them ?, and what folder have you told CC to place them in

when the book has been "lost" is it actually still there but in a different folder - if you search on device with a file explorer / does it appear in documents using the fire tablet docs app, or in books using the tablet's kindle app

i.e. are the book files being deleted or are they being moved ?

i assume you don't have paid for copies of these specific books in your amazon cloud, because if you did, there would be no need for CC to transfer - you'd simply read them via the books tab ?
and that no other restrictions apply to the books e.g. they are not time-expired loans

Also you could test again, but with CC removed from the test sequence i.e. connect tablet via USB, open it in windows, and copy the same books to the same folder that you were using with CC

then proceed to read, do other stuff, read again, like before.
for the 1st read, navigate to the tablet folder where you placed the book, with a file explorer and use open with to open it in kindle reader, if a double tap does not do that automatically.