Most likely, there is an offline copy of the project with no comments and it is a better match than the one you want to "upload and use".
There are a variety of methods to deal with this.
1) Export the comments and then import them into the online copy. This won't get you any CDM or CGM files. Later, you can drag and drop those files (or copy and paste them) from the "good" file to the new matching file.
2) Move the better matching file with the blank database to another location outside of the default search path. Then go online again and you should be prompted to find a matching file. Then you should be able to browse to the one you want and upload and merge with its database. This method will retain anything else in the project like CDM and CGM files.
