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DelennDax7 - first you can Merge the PDBs and EPUBs into one 'book', sort them on title and author, select a pair of lines in the Book List and press 'M'.
You could create a Virtual Library for the PDB's with this search term
Then you could use the Save to Disk feature within that virtual library to save all the PDB's to wherever.
But, why do you have to move the PDB's. I am not familiar with eReader Pro and I'm not sure I've ever seen a PDB - so the following is guesswork, and assumes you're using Windows.
Assuming you can associate the PDB file type with eReader Pro (double click a PDB in Windows Explorer, if it asks how to open, Browse to eReader Pro.exe and select it), then
uncheck PDB in the
Preferences->Behaviour->Use internal viewer list for: list.
Now, when you view the book from within calibre (press 'V') and select the PDB format the eReader Pro program should spring to life showing the current book.
BR