Hi John,
Running SS with Sim running shouldn't screw anything up....you just get the error notifications and the files are not switched.
First thing I would do is run the List Seasonal Files.cmd file again and go over the list very carefully. It is very rare to have done something to your seasonal files that can't be seen by running the List Seasonal Files.cmd file and studying the resulting list which you can also print out to study more carefully.
If in fact, you still can't see any anomalies as described in the instructions that come with the List Seasonal Files.cmd file, post a screen of the exact error message that you get when running the Season Switcher. In addition, let us know the structure of your RTMM Scenery directory beginning with Addon Scenery folder and note where the Season Switcher executable that you run is located.
You might also upload, as an attachment, your resulting list from when you run the List Seasonal Files.cmd file so that I can take a look at it.
Rod