Thanks again Chaley for your help and the info.
On my Fire I moved all the apps back to the internal memory, then uninstalled calibre companion and unmounted the SD card. I then redownloaded calibre companion and connected the app to my MAC. This time i moved all the 4500 txt files in small batches and it all worked smoothly only taking about half an hour. Hopefully i won't hit the problem again as going forwards its just adding new purchases.
I'll do the same thing again if i get issues in the future. Thanks again for your help.
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