Strava keeps track of your activities, and tries to prevent you from uploading the same activity twice. If you're modifying a file using GOTOES, you might want to keep the original file in your account and make sure the GOTOES file is what you want before you delete the original.
To TRY and upload a duplicate activity, you should check the "Randomize ID Tag" option. This option is selected by default (though the tool will "remember" if you de-select it for future merges). This slightly changes the time of your activity. It can have a VERY MINOR effect on your speed, elapsed time, and moving time. If you don't need to upload duplicates to Strava, you are free to un-check that option.
The reason I say "TRY" is because sometimes the shift that GOTOES applies is not enough to escape the Strava duplicate activity detection algorithm. You can try again by just clicking the big blue "Click Here to Process the Files Using Above Parameters" button (you can click that more than once). DON'T REFRESH THE GOTOES PAGE... Each time you click that button, GOTOES will export your file - and each time it will increase the amount of random time shift. If you refresh the page, though, the entropy will reset to the original values.