For test purposes, I created a new project. Search worked fine in Webhelp generated from that project.
Here's what I did.
1. Create a new blank project.
2. In Project Manager, add New> Folders to the Project Files folder, being careful to copy the folder names from my most recent project.
3. Imported topics into each folder from my most recent project.
4. Imported the Table of Contents from my most recent project (New Table of Contents, Copy existing Table of Contents).
5. Imported the project skin on the Project Set-up Tab from my most recent project.
So far so good. I risk breaking links and can no longer see the creation date on my topics, but at least I have an operable search.