I wonder whether the "Exclude" tag actually exists in the project to which the topics have been imported? If not, try adding it and then removing the tag from the topics and finally deleting the tag. If this doesn't work you may be forced to enter the dark side of HTML and remove all the <meta name="build tags" content="Exclude" /> meta tag from HEAD section of each topic.
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I tried both suggestions and neither worked. The tag was definitely part of the project, and even when I removed the HTML, the topic still displayed the hash marks as having a conditional tag, though in the properties dialog none of the tags was selected.
So I looked at the project folder in Windows Explorer and discovered that the offending topics were present in two different locations. One location was a folder within the project manager (which is where I'd been working) and the other location was at the top level folder for the project. I think the person who last worked on this project imported the HTM files to the wrong level or something and didn't replace the original versions of the topics. So I deleted the duplicate topics and was able to deselect the conditional tag from two of the three offending topics. But not the third.
Then I looked at the properties for the conditional tag and it showed that it was being used at the <Topic> level and the <Content> level for the topic I couldn't change. So I check the folder in project manager (right click>Apply Conditional Build Tag>New/Multiple). The dialog showed that Exclude was selected, but it was kind of grayed out. So I clicked Clear All, which seemed to do the trick.
So maybe it was a combination of having duplicate topics and having the conditional tag associated with the folder as well as the topic? In any case, it seems to be OK now.