First - I'd make a back-up of your site somewhere in case this ends up destroying a bit of your data, but this got me to be able to edit your maincontent.
select a folder/or your whole site, and do a search/replace.
choose, "selected files" or "entire current local site" put this in the search for box:
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<!--THIS IS THE MAIN CONTENT AREA; WDN: see glossary item 'main content area' -->
<!-- InstanceBeginEditable name="maincontentarea" -->
<!--THIS IS THE MAIN CONTENT AREA; WDN: see glossary item 'main content area' -->
<!-- THIS IS THE MAIN CONTENT AREA; WDN: see glossary item 'main content area' -->
And leave your replace with box empty.
Hit "replace all"
You'll get a warning saying something like, "this operation cannot be undone in unopen files" (which is why you should backup to be safe) - click ok/proceed, and it should get rid of the duplicated comments.
If all the pages have this same duplication, you should be able to edit your whole site, if not, find the duplications and do the same steps for each.
You have to have the files unopened for the search/replace workaround to work - its the only way to really trick dreamweaver into editing the non-editable sections - or you could go back to your old editing program and make the changes and import the site back into dreamweaver.
Just make sure your pages only have one:
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<!-- InstanceBeginEditable name="maincontentarea" -->
in a row before each "end editable" - that's where the problem was.
Hope it works, and if there are any other pages you need looked at, let me know.
Bryan