The list of recently read books is kept in a simple text file called
lastopen.txt and is stored in
directory
/system/state in main memory.
If you connect your PB360 to the PC and open lastopen.txt in a text editor you could manually (and carefully!) remove the lines for books you no longer wanted to appear as 'recently read'. Alternatively, if you delete books from the PB360 after reading them they are automatically removed from lastopen.txt as well.
As for whether this is a good practice -- I'm not sure
The only other option I know of is to use Settings - Maintenance - Clean state. But, this clears all books from the 'recently read' list.