I can understand why "assets" folders aren't backed up in the .bak folders. Doing so would create a huge mess and eat up disk space unnecessarily. In fact, I recommend [i]never[/i] saving with assets unless you need to make your project "portable" (take your project data to another studio to work on). Here's my procedure:
1) when starting a new song, save with the assets checkbox ticked. This creates an Audio Files folder within the project folder, but not a Bounces folder.
2) when saving the song again, whether it's under a new name or the same name, assets = unticked.
3) when bouncing, you have the option to manually create a Bounce folder in the file selector and save your bounces in there, or, not. Bounces don't have to live in a "Bounces" folder, but it is a convenience.
That's all there is to it. The result: all assets which are unique to the project live in the project folder (audio files, bounces). All assets which are not unique to the project (and which already live on your system hard drive such as factory EXS-24 and UB samples, impulse responses) remain in their original locations.