The more I'm hearing about intermittent loss, the more I think you should be asking for help in one of the calibre sub-forums. There's a better chance that one of the calibre technical guru's will see it over there. If this was a common problem I would have expected to see many similar posts about 'disappearing' plugboards.
I can't reproduce the error and as most of my readers are Sonys I can't replicate switching between Sony, Kindle, Kobo, Nook etc. I can switch between Sony and PocketBook, but that hasn't caused a problem to-date.
What I'm finding hard to understand is that if you have added both PRST1 plugboards, the main 'device_db' one and the backup 'epub' one, then the latter should physically force the plugboard data into each epub as it is sent-to-device or saved-to-disk. It's hard to see how a calibre connect/disconnect cycle could physically remove it. If it did and you had hundreds of epubs on the T1, every connect/disconnect cycle would take ages.
For the more technically comfortable, from what I see (rather than what I know), if you unzip one of your epubs on the T1 (not in the calibre library) and view the contents of the
.opf file in a simple text editor, the 'epub' plugboard data seems to be contained in the
<dc:creator> line in the
<metadata> section, e.g. see red bit
Code:
<dc:creator opf:role="aut" opf:file-as="Christie, Agatha">Christie, Agatha - Poirot 15</dc:creator>