For better or worse, I have adopted the habit over the years of saving projects in stages (with descriptive names) and have inherent distrust in every scenario being tried/tested in development. Prior to major changes (especially destructive ones), I will save just in case, then can just close the project without a save and reopen it.
 
I realize this may rub some the wrong way, but reliance on "bug free" software (anywhere) is folly.
 
 

I'd report it to CW through the proper channel if I were you.

I think it's reasonable to assume that an "undo delete synth" command would put the track back the way it was. Are there other things that won't "undo"? I can't remember reading about it in the manual, or seeing it in any of the tutorial videos about the synth rack that I've watched.
Guess you will have to be a little more careful about synth deletion in the future sharke, certainly until Cakewalk can fix the issue. Or if they don't/can't, then a change of workflow is the only option.
Thanks for posting this, it's something I can at least understand when and if it happens to me.

Double post sorry.

My view it's a bug and should be reported via cake problem reporter (please let us know the number).,Why is it a bug? Because undo does not undo correctly. If it was incapable it should not undo at all or it should produce a warning telling the user that it won't fully undo.

Cake are apparently aware of the problem. So we can only assume that it will be addressed in a future update. 

So from the sound of it that means it's being regarded as a feature request as we have no problem reporter number.