I am sorry to hear the everybody is having so many problems with CDSD3.
Let me respond to some of your concerns, providing some background and explanations.
No, SoundSoap was never an optional plugin for CD Spin Doctor
This is indeed very unfortunate. The problem lies in SoundSoap. Yes, I know, now you're thinking "the blame game". Not so. CDSD, since version 2, uses Apple libraries for reading sound files. Easier for us to maintain. If the library says it can't read the file, then neither can CDSD. Apple's libraries aren't as lenient as other libraries.
We did at some point have limited support for well-behaved VST plugins which hosts their own UI. Unfortunately, SoundSoap is not well-behaved, and neither is a lot of other VST plugins.
Not quite true. It wasn't just SoundSoap. If you feel adventurous you can still add plugins to the application plugins directory, though officially not supported, it should work in most cases, and if it doesn't, just remove the plugin. We just don't look in the sanctioned OS locations for VST pugins anymore. Too many issues with non-standard VST plugins.
See prior comment. Toast uses its own libraries for reading and writing audio files. Are you saying that CSD3 renders the file unusable by any program after failing to open it?
As far as fixing any file related problems, we might be able to mitigate reading (read: repair) damaged supported audio files. That would require samples of audio files (small ones) before and after damage has been done. We're asking for your help to make CDSD even better.
Hosting 3rd party plugin UIs is not a trivial matter. Without going into technical details, in this case, from a programming standpoint, it would be like mixing apples and oranges (no pun intended ;-).
Would it be possible for you to send us a file which displays this behavior to us at Deep Sea Software? We would need the file in three copies: after recording (no processing), after SS2, and after attempting to open the file in CDSD3. Please upload, using anonymous ftp, to ftp://ftp.deepseasoftware.com/incoming
If you do, please drop a line to support [at]removethisdeepseasoftware[remove this].com