Yes, I hate to say this, but that's way too many titles (especially those PDF memory hogs!
), than the Reader can comfortably handle.
Any time you want to add or delete titles, you're going to have to wait an agonizing amount of time; but, even more so, with that many titles, you risk the danger of something going screwy somewhere.
My advice is to cut down - drastically - the number of files on your Reader. This concern is echoed almost universally here. Most of us here put between 100-200 titles on our Reader.
The constant loading and unloading will also drastically reduce your battery life.
Also, let me welcome you to MobileRead.