Are they broken links or missing topics?
If they show up as topics with a red x in the icon, I think you should just be able to click Restore. If the whole folder is missing, you should just be able to Import and select all the topics in the applicable folder.
If they are broken links, you'll have to fix the reference in the applicable topics. Right-click on the link and select Show Topic References. The dialog box will list all the places that the topic is reference. Click Edit and locate the link or Related Topics button that references the topic and fix the link. For index and TOC entries, you can just fix the link in the dialog box that opens.
Did you by any chance tried doing multi-File find and Replace through any third party tool, or did you tried editing any of the .fpj file manually? and do you see those topics physically present inside your project.
can you please share the snapshot of the broken link list and the "root.fpj" with me
I couldn't fix the links through Tools> Resolve Broken Links for some reason. So, since it was only about 8 htm files in one folder I imported the files and created a folder with the same name. Then I deleted each broken link and Rh allowed me to do this.