I did indeed make the backup.
However, I suddenly remembered that one of my colleagues had a simlar problem some time ago and we solved it by re-creating the topic sub-directories under HTML Files (Topics) in the Project Manager - then it was possible to restore the files from the Broken Links directory. This worked in this case with the exception of one file (the one I guess I was working on when it crashed) and this I just restored from the backup.
While using search and replace you should be very precautious as you might change content of some other project files (like .fpj which contains the folder information) file rather than HTML files and in such scenarious you might be corrupting these files and the project itself and you might loose all the files that were in the folder, the .fpj files of which has been corrupted, this seems to have happened in your case.
so if you are using a third party find and replace tool then you should also use a proper filter like (.htm) or the same can be achived form the RoboHelp Find and replace tool (inside Edit menu) and using .htm filter the default filter.
Hope this helps you in future