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Before trying to meticulously restore link after link, try clicking Tools > Options... > General tab and enabling the option to Clear project cache. Then close and restart RoboHelp and open the project again. You might find yourself pleasantly surprised with the outcome.
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I have seen the same thing happen in RH8. In my case it was after renaming a project. Using Restore did correct the problem and it did not come back. Alternatively, you could create a new project and import the content but that will likely take even longer.
In my case, Rick's suggestion did not fix the problem but it is definitely worth a try. Personally when I do use the new check box, I clear it after use.
See www.grainge.org for RoboHelp and Authoring tips
Thanks for the suggestion. Seems like a plausible solution, and I'll try using that setting going forward. Sadly, it did not help me with this project.
As it turned out, restoring the links manually was my only solution. It didn't take quite the entire day, and by frequently trading off my mouse hand from right to left, I didn't go completely carpal on either wrist in the process.
Although this was not the answer I was hoping for, it at least helped me resign myself to my fate, and that did help.