Before you start, make a backup of the Scrivener project. That way you’ll at least keep what you have if something goes wrong.
In the Google Docs version of the project, locate the Comments files. Use the Download As -> RTF option, and download them to a convenient location. Use Finder to change the extension back to .comments.
Also in the Google Docs version of the project, locate the .scrivx file. Download that as plain text, and save to the same location as the comments files.
Open the .scrivx file you just downloaded in TextEdit. It’s raw XML, so don’t worry that it isn’t terribly human readable.
CLOSE SCRIVENER. We’re about to mess with the project behind its back, which is potentially dangerous.
Locate the new project in Finder, right-click, and select the option to Show Package Contents. Locate the .scrivx file, make a duplicate, and drag the duplicate out to another location. Open the duplicate in TextEdit. (You’ll need to use the Open With command to keep OS X from trying to open it in Scrivener.) Then, browse to the project’s Files/Docs subfolder.
Open another Finder window, and browse to the folder where you put the comment files from Google Docs.
You now have two TextEdit windows, with two different .scrivx files. Select all of the text in one of them and change it to a different color so that you can tell them apart.
A bit of explanation: When Scrivener imports or creates a file, it assigns a number to it. 54.rtf. 32.pdf. And so on. All secondary documents associated with the main file will carry the same number. 54.comments, for example, or 32_synopsis.txt. The scrivx file is a master index that ties the numbers to the human readable names that you see in the Binder. If you transfer a file from one project to another, it will get a new name in the new project. What has probably happened here is that the comments files no longer have the same number as their associated RTF document, and so Scrivener doesn’t know how to connect them. So, here’s what to do.
Look at the comments files that you downloaded from Google Docs. Pick one, let’s say it’s called 56.comments. Open it in TextEdit (again, you’ll need Open With), but don’t change anything. In the .scrivx file for the backup of the project (the one you downloaded from Google Docs), search for the phrase: ID=“56”
You’ll find a chunk of code that starts 'BinderItem ID=“56” ’ and continues for a couple of lines. Copy the text after ‘Title’ in that block.
Switch to the .scrivx file for the new project, and search for the title you just copied. That will tell you the item’s new ID number in the new project. (42, let’s say.) If 56.comments is present in the new project, open it in TextEdit to make sure it has the same contents as the one from Google Docs.
Close both comment files in TextEdit. Either rename the one currently residing in the new project to 42.comments, or rename the one from Google Docs and drag it over.
Open Scrivener, use the Title to find the appropriate file, and confirm that the comments re-connected correctly. Assuming they did, close Scrivener and repeat for the rest of the files.
If you have a lot of comments, you may encounter collisions: 42.comments already exists, but it has comments for a file other than 42.rtf. You can use temporary names as needed to “store” these files until you find their parents. I’d suggest something like a_42.comments: a real Scrivener comments file will never have a letter in the name, but you’ll still be able to use the item ID number to find it.