When you make any changes in the Transcript Editor, they are not automatically applied to any of your existing Caption Files. If you want to pull these new edits into your existing caption files you will need to Resync the caption file. After you edit your transcript in the Transcript Editor, go back to your project page and refresh. You will then see your caption files go from a green completed status to a gray out of sync status. To pull in the changes you just made in the Transcript Editor to your caption file hover over More Options and click Resync.
NOTE: any styling, positioning or caption segmentation changes will be lost as the project will resync with the new data.