This is probably due to the fact that the output streams for the log files for Data collector monitors and Write-in-file monitors are not flushed regularly.

The output streams for monitor log files will always be flushed at the end of a simulation if the Fast forward tool is used to run a simulation, or if the simulation stops because a breakpoint monitor is fulfilled.

If you use either the Bind manually, Single step, or Play tool to run a simulation (and no breakpoint monitors are fulfilled), then there is no guarantee that the output streams for monitors will be flushed during the simulation.

Why can't I generate a state space for a timed net?
Are bounded places supported in CPN Tools?

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