I have calibre that I've used rarely for problems (long story but I got help here on fixing some ebook problems) and maybe that's the way I should go.
I don't know though if you can set it up to automatically work when the reader is plugged in, or is it more a manual thing?
Either way, calibre is kind of confusing.

It seems very functional but harder to figure out what's going on with it. But if I can, and can get over it looking so much less good-looking, it might be a better way for sure than these awful Sony softwares.
~
And the saga continues...
(and a new important question coming up)
So, it's taken me, what, a week now, but I finally have a bit of good news (although, of course, there's a problem with the good news...).
First, before that, let me say I did contact Sony support by chat. Much better than by phone and the person seemed pretty helpful, at first anyway.
He wanted to direct connect to look at the problems, so I let him even though it felt dangerous and invasive to let him have all that access to my computer, but oh well.
So let's review what I got out of the THREE+ HOUR help session:
I told him I had four problems, and we went one by one.
Problem 1 as told by me - Syncing Reader for Mac with Reader Library deleted half my library and the accompanying notes. I know I can re-download the books from the store or internet, but all my notes are gone. Can you help recover them?
Resolution from him - *after an hour and a half of him snooping around and trying things on my computer* There is no way for the software to delete your files. Your solution will be to re-download the books.
Problem 2 as told by me - While you were looking you already noticed the non-stop pop-up about a "syncing error". Can you stop that?
Resolution from him - *after awhile and after eventually trying to start deleting things on my library at which point I had to fight for control of the mouse to stop him* Your solution will be to delete everything off your library, delete the program and then re-install and re-download all the books.
Problem 3 as told by me - The Reader for Mac window cannot change height and width together. I can press the green button and the height decreases a little but that's it. Can you help?
Resolution from him - *after ten or twenty minutes of trying to change it himself* The software is not designed to do that.
Problem 4 as told by me - The Reader Library is extremely laggy for me. Can you help?
Resolution from him - *he opens it back up and somehow, when I didn't realise, he had deleted everything off my Reader Library (it was still all on Reader for Mac although I caught him about to delete all that earlier too), so there are no list of books to scroll through and lag with* It appears to me your Reader Library is working very fast.
So yes, basically three hours and not one of my problems were fixed.
The second help, to delete everything and start over, I'm in the process of listing everything and saving all my notes first so I can't do it yet, but I will. Though I'd already thought of doing that myself anyway after safeguarding everything. The other three helps were complete busts.
I was especially annoyed that he deleted everything from reader library (I think when he was doing some jiggying around in the Finder files area so I didn't realise he was deleting Reader Library) and that he was about to start deleting everything off my Reader for Mac! Anyway...
Time for a little good news -
Today I've been trying to list everything separately and save all my notes and such and was almost finished when an idea hit me -
My 950 has an SD card. I got help here at mobileread awhile ago about speed issues on my 950 and part of the help was to get an SD card and store everything on there instead of the 950 hardware.
When this current problem happened, things were still on the SD card. I described my problems even getting the Reader for Mac to recognise the 950 at all, and when it did, it apparently erased all the books that were also erased on the Reader for Mac.
Oddly though, Reader for Mac doesn't open up a separate little panel, as far as I can tell, for the SD card like it does for the 950 when I plug the 950 in, unlike Reader Library which would open up tabs for both the 950 and the SD card.
So I noticed that today, that there was no SD card panel showing up and it made me wonder why not. I still haven't figured that out, but I took the SD card out of the reader and put it in my computer to see directly what might be on it and not showing up.
JACKPOT! Kind of. Apparently, Reader for Mac did erase all the BOOKS off the SD card, but not the annotation files! They're all still there! And that includes every important book with notes that I had except for only two. It's still sad to lose all my notes for two important books, but that's way better than losing notes for like 20 or 30.
BUT there's a problem. Of course, heh. Nothing can be so easy. I can't make any use of the files.
I tried clicking to open them and they open in text edit, but not in any useful way. They are loaded with so much crazy code it's basically unintelligible.
Here's an example:
Spoiler:
</content>
<sony:data xmlns:sony="http://www.sony.com/xmlns/product/prs/adeannotations">
<sony:item name="identifier" value="prsID.2.highlight:60-0-0-dGV4dC9wYXJ0MTgueGh0bWwjcG9pbnQoLzEvNC8yLzIwLzE6NT IwKQA=-dGV4dC9wYXJ0MTgueGh0bWwjcG9pbnQoLzEvNC8yLzIwLzE6NT I3KQA=" />
<sony:identifier>PLEASE IGNORE</sony:identifier>
<sony:item name="duplicate" value="false" />
</sony:data>
</annotation>
<annotation>
<dc:identifier>urn:uuid

00005FABA9E-14FA-9632-7E3E643B081D</dc:identifier>
<dc:date>2012-04-28T18:01:42Z</dc:date>
<target>
<fragment start="text/part18.xhtml#point(/1/4/2/152/1:3)" end="text/part18.xhtml#point(/1/4/2/152/1:240)"/>
</target>
The text of my notes are mixed in there here and there but it's extremely hard to find them. And then, the actual highlights aren't there, just my notes on the highlights (although plenty of highlights didn't have notes).
But, I've surmised that all that gobbledygook must be some kind of code for where the highlights are in the book so I think I have the codes to all my highlights and notes, I just need to be able to use them!
So I thought of re-downloading a book and adding the appropriate file to the book. I picked one and did it. I re-downloaded it, added it back to Reader for Mac then added the annotation file (and the Reader for Mac let me add the annotation file) but when I opened the book, no luck. There are no notes or highlights for it. And it was the exact same book as far as I can tell.
Soooo....
Major question -
Can anyone help me figure out how to make these annotation files useful? Any way to get them to work right?

And again, thanks so much for any help with my saga!