Let me shed some light on this. After you close BeerSmith, it continues to operate archival features in the background for a short period of time. Shutting down the computer, forced restarts, or low power shutdowns disrupt this operation. When you go to restart BeerSmith, it reads that the archives are still being updated or that some of the archives are missing and assumes that the program is still operating. This is what gives you the error message. You can force open it and may find that as some of the archives are missing, you have lost some of the files or folders (usually recipe related). Brad has put up a blog on how to recover the missing archives and commented on another thread that he is looking into how to protect the files from this issue occurring.
I don't know if this is the exact same for Macs as it is for Windoze computers. I used to keep a running copy of BeerSmith open to quickly look up commands and procedures to answer questions here on this forum and others, but now shut it down when not in active use. I have not had an issue since adopting this practice.