While it should be set up to overwrite existing pages, there could be something with how it is reading the edited files that could be causing it to duplicate instead.
If you are fixing this by editing the HTML to remove the text string, you can edit the HTML from within Canvas. If you know the exact pages that the text string is located on, even better. Go to the page needing removal of the string and enter the editing mode. Then click on the < > icon in the lower right below the editing pane to access the HTML editor. Now, there are two versions to the editor: Pretty and Raw. Once in the HTML editor, you can switch between them with a button on the left side below the editing pane. The Pretty version indents everything, but doing CTRL-F is limited to just what is visible plus a few extra lines. If you have a longer page, switch to the Raw editor and use CTRL-F to search for the string. Then remove the necessary part and save. Try this with one page you know has the content needing remove to see if you can find the necessary string to remove.
A benefit to this method is saving the steps of needing to export, unzip the .imscc file, edit files, rezip as an .imscc file, then import the file (and any necessary fixing of duplicates). Plus it means that you can now export a clean file with the issue fixed.