If workflow settings and .replit file are not synchronised, then changing one gets overridden by the other, making it impossible to change either. You also ge tweird behaviour like the stop/run button not reflecting what is actually happening, and the console log seemingly stuck and never clearing. It’s a mare if it happens to you!
This happens when Assistant creates workflows for you, eg a workflow to hard reset the environment. Or if you restore a previous .replit version.
The way to solve it is to delete the .replit, and the system will pop up an error message that your environment needs resetting. Then manually add back ports etc to the bare-bones .replit file.