You haven't said which version of RoboHelp you are using.
Do they show in the Topic List? If not when you generate it should clear the target folder, if you publish they don't get deleted there.
I am also wondering if it is a cache issue. Use the browsers Refresh or press F5.
I am using RoboHelp version 22.214.171.1244. I have cleared the browser cache and even closed/reopened RoboHelp and it still shows. The deleted files do not show in the TOC, but if you search for specific keywords that were in those deleted files, the deleted files show in the search. Additionally, if you click on that item in the search it open that supposedly deleted file! Thank you.
You haven't responded to my question about the Topic List.
Try generating to a different folder.
No, the files do not show in the Topics list.
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OK try the new folder.