But you did find the files, you just could not open them...
I still wonder what the "PATH:" on long taps says in such a case.
In your case I would connect calibre to a folder on your Kindle (not connect to device but connect to folder), because then you can send the EPUBs there. And if you do that really in a different folder (not mnt/us) you would have two metadata.calibre and could use both at once.
The search function only works with metadata.calibre, it does not search through your file system.
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