What you are encountering is not an issue with having two licenses (which I will address later) but due to an unexpected shutdown of BeerSmith. When the program is closed, there are a number of archival operations which happen behind the scenes so to speak. If you have BeerSmith open when, for instance, Microsoft decides that it is a good time to update your software, the program will close and Microsoft will start its updates without allowing the archival function to run. This leaves a flag in the system which then thinks that some element of BeerSmith is still operating and gives you the error when you try to start BeerSmith.
The other result of this is that the recipe and profile libraries are interrupted in the archival function and the some of the recipes can get lost. You can recover this lost information as Brad describes in his blog post which can be found at
http://beersmith.com/blog/2018/09/14/how-to-back-up-and-recover-data-in-beersmith-3/This issue has led me to change my behavior with regard to leaving my cope of BeerSmith open on my computer. Where I used to keep it running to be able to access it frequently throughout the day, I now shut it down when I am not planning on using it for a while.
As for the licensing, if you check on the BeerSmith FAQ page, I think you will find that a single license allows users to download the software onto up to two computers or devices.