Please note that Vista uses virtualization for all pre-5.0.1 versions of PhpED and therefore you need to backup files configuration files located in "C:\Users\YOURACCOUNT\AppData\Local\VirtualStore\Program Files\nusphere\phped\". Note that non-english Vista distributions may use different path for virtualization.
After you installed 5.0.1, you need to copy configuration files into "C:\Users\YOURACCOUNT\AppData\Roaming\NuSphere\PhpED\config\" directory. If config subdirectory is not created, please create it first.

In my previous version (5.0) I had redefined the NuSphere project directory to another disk/directory (d:\nusphere\projects) because of disk space reasons. The new version is really confused now.
It tries to save the .ppj file to C:\Program Files\nusphere\phped\Projects although I opened it from the D-disk???!! I want all my projects to reside in that D: disk directory!

And, after the upgrade, every item in my Accounts list is lost and I will have to redefine it. Or can I recover it from my D-directory?

What can I do?

Yes, I am using Vista...

I think that all the config files you worked with, including accounts.cfg are in
C:\Users\YOURACCOUNT\AppData\Local\VirtualStore\Program Files\nusphere\phped\
just copy them to
C:\Program Files\nusphere\phped\

Regarding where to store ppj files, it's up to you. After you saved ppj into desired place, IDE will not bother you with this file anymore.

Why was all my config deleted when I upgraded to 5.2 today??