When you are running a simulation using the Analysis ⇒ Simulate command, the Sonnet project is locked until the analysis is complete. You may not make any changes or execute any commands in the interface until it is unlocked when Sonnet is closed.
If for some reason the analysis engine is interrupted in such a way as to prevent a graceful shutdown, such as a hung program or a program crash, then the Sonnet project is not unlocked. In this case, you may manually unlock it by selecting Analysis - Unlock Project from the main menu of the Sonnet Cadence Virtuoso Interface window.