Estop is activated by one or more of your inputs. Now whether or not you have anything written in your estop.fil does not really make any difference, the Estop condition will still occur, and the control will check to see if there is something it should do, in the Estop.fil. However, the input will still have to be cleared by the releasing of a switch or something.
Possibly you could have Estop triggered by flags set in certain variables, too. You might go through and check where every variable is being used, to make sure that you've not accidentally used the same one for two different things. I think you do this by doing a variable search, and Camsoft goes through your files and shows you a bit of logic with that variable involved, so you can look at it and begin to figure out if you've gotten an ambiguous callout.
Another way is to backtrack to a previous version of your cbk where you did not have this problem. Restore it and begin from there. I hope you do not continually overwrite your cbk file. You should keep a series going, and save your work to a new cbk whenever you have done a lot of programming.