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In each RH project you can run an "Unused File" report that identifies all files (not just .htm files) that are no longer referenced anywhere. Provided your topics are no longer linked to, indexed, in baggage or have some other reference they will show up there. Just delete them in Windows Explorer. The reports are available from the Tools menu.
In the Topic List pod, enable the TOC column if it's not there already (right-click the column titles and choose TOC). Then click the TOC column title to sort by that column--all the topics not in the TOC will be sorted together by "No." Then you can select them all using Shift+click and then delete them.
Another option if you're not prepared to totally blow them away would be to create a conditional build tag called something like "Unused." Using the same method above, locate and select all the unused topics. Right-click them and select Properties. On the Advanced tab, apply the Unused tag. Then, in your single source layout, set a conditional build expression that excludes the Unused tag. Those topics will be kept out of the output and out of the search.
In RoboHelp 8 you have the ability to display the Topic List pod. In that pod you have an option of viewing which (if any) TOC topics are a part of. You could click the heading to sort by TOC and see which topics aren't part of any TOC.
If you just want to hide them from searching, you could select them and display the properties. RoboHelp 8 has this way cool new feature whereby you may indicate at topic level whether it should be included in a search. This is done using Topic Properties on the General tab (I think - RH8 isn't in front of me at the moment)
Hopefully this helps... Rick
@Ben: That was perfect, thank you! The pod was exactly what I was looking for.