To add on to Chris's statement, you cannot do what you want to do, period. If you export and change the HTML files, you will lose any work if you import it because the app does not recognize your changes in HTML AND you have to then edit it manually and will lose all functionality for drag and drop. The app is not meant to be a partial setup in that you export and import files (other than JS and CSS), it's meant to be either:
Create your structure, export and finish your site from now on outside of BSS
or
Create your site and maintain it within BSS always.
You CAN however, export your site, edit your JS and/or CSS (for whatever reason you could possibly need to do this) and import it back in. That works, and that will not lose file content EXCEPT for comments which are not usable in BSS at this time. If you add any to an exported CSS file and then import that CSS file back in, all comments are gone.
So ... as Chris said, why are you even editing anything outside of the program and then expecting to re-import it? Just do it in BSS and be good to go!