I've only had my PRS-600 a while now and congratulate you on your possession..
I had troubles with my old memory stick (upgraded from PRS-500).. I was forced to salvage all ebooks from the memory stick, delete everything, then reload the books using the Sony software. This worked for me.
I have not tried out the limits of the PRS-600 for ebooks (although it is very tempting and I have plenty of ebooks to do so). Currently I've got 251 on the Reader - either on memory stick or in internal memory.