File a bug please. I couldn’t reproduce. I unzipped a 2.6GB zip file of 81 flac files into an indexed directory, and baloo immediately started indexing the file contents and within a few minutes baloosearch could find the files searching by metadata and balooshow -x showed the music file tag information. I had turned on baloo debug output and the journal indicated a dozen files were indexed twice by different baloo_file_extractor processes, but all the info was there.
If you had an incredibly large zip file or very slow unzipping it could happen. But there are so many variables with file systems (I’m on btrfs), zip programs, file contents, how busy your computer was during unzip and indexing, etc. it’s hard to know what’s key to causing the bug.