I haven't seen this before. Looking at the code my suspicion is with the pid files we keep under $HOME/25.0.2/instances. If something prevented the file from being deleted when the editor exited, and another process took this PID, AND our checking missed the fact that the process wasn't a SlickEdit, then it would cause what you're seeing. I don't see another code path for that error. I've only taken a brief look at the checking and cleanup code, and it doesn't look obviously wrong, but I need to take a closer look later this morning.
Have you had any crashes, or had to kill the editor with kill -9 or anything like that?
In case I don't find anything, here are things to check when it happens again:
1) When this is happening, do you have another instance of SlickEdit running? Running vs without +new implies there may be another editor you want to open the file in. Check the process list and make sure that the number of vs_exe processes matches the number SlickEdit editors you have running. In the unlikely case where there's a editor that got stuck cleaning up after it closed the main window.
2) ls $HOME/.slickedit/25.0.2/instances. There will be files whose names are PID numbers. Do you have more than actual open editors? With your editors all closed, are there still files there? If so, do any of them match the PID's of any running processes?
Once you've checked that, you should be able to recover by closing any running SlickEdit windows, and then just removing the contents of the $HOME/.slickedit/25.0.2/instances directory, rather than the entire config, unless I've completely missed what's going on.