you can use the WorkflowManagement.aspx in the folder to see what tasks are running.
Its my understanding that if you publish over an existing project, the tasks already running will try to run the new code, but
depending on the changes you made you may have a problem.
If you changed the logic or added variables, the existing running tasks will not have that information and may crash when
the get to that part of your app.
If you made simple changes like fixing spelling or text on a screen you should be OK.
the general recommendation is to not publish over an active project, and use some type of versioning to control
what path you application will run and it runs only that path until completion.