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The real project should not be a problem as I have several projects around that size. More likely the CPD file underpinning the project has got bloated and just needs recreating. See the article on my site about Opening Projects.
You sat down and created 10,000 files to test this?
I programatically created 10,000 HTML files and a HTML Help Workshop project and imported it into Robohelp.
Once it became a real Robohelp project it was totally unusable.
HTML Help Workshop compiled the original project without problem.
My existing project will continue to grow for perhaps the next 10 years at the rate of 1000 topics per year. If Robohelp isn't going to cope then I need to find an alternative solution within the next year.
You could try deleting the CPD in the 10000 file project.
I wouldn't like to say RH cannot cope with 10000 topics. Back in version X3 the PC I had then was slow around that level so I split the project and used merged webhelp. To the end user that is seamless, for us it means faster projects. Projects larger than 4000 were still usable, just a bit slower as they got larger. 10000 was still usable but sluggish.
PCs are now faster so that would be less of an issue. Try renaming that CPD and let us know how it works then.
I deleted the CPD in my 4000 file project.
Robohelp took 30 minutes to rebuild it and now I have several hundred broken links.
There is something fundamentally wrong here as it should not have that effect. Hopefully you took the backup as per the article on my site.
Have you created all the topics within RH in the normal way or were any shortcut methods employed?
Anything else unusual about your use of RH?
Is the project on a network, other than via source control?
Are all / many of the missing target files in a folder that is not showing in Project Manager?
Project started life as a 1000 topic HTML Help Workshop project along time ago by someone else.
I imported it into Robohelp 6 a year ago and since then I have added another thousand topics.
All files are local.
As you suspected, all of the missing target files are in folders that are not showing in Project Manager.
This has happened before for me too - I just recreated the folders, imported the topics back into them, and all was well. This happened after a CPD rebuild as well.
I considered it a good thing - I am convinced that CPD bloat and the attempt to reconcile file and folder locations was slowing down the program significantly. The CPD just needed to be rebuilt. Of course, I have a large project, and it took a few hours to get back to running speed, but yours is about twice the size, so you will be down for awhile.
If I were you, I wouldn't necessarily consider returning to the backed up dataset right away. You'll be back to the same performance issues. In your shoes, I would suck it up - just rebuild what needs to be rebuilt, and move on. And keep an eye on your CPD file size occasionally. I find that if the file size increases significantly all of a sudden, it's probably time to rebuild it.
You may want to consider Peter's suggestion (reminiscence?) of breaking up your project into usable chunks and merging them.
That's my two cents, take it for what it's worth.
You might find if you just add those folders in Project Manager, RH will do a little dance and the files will add themselves. You may have to just import the topics back in. You can select multiple files within a folder.
I spent 2 days manually rebuilding the broken links as Robohelp made zero attempt to resolve them automatically.
The project load time has improved. I'll see how it goes for the next few days.
Also, as an exercise I deleted the rebuilt CPD and again hundreds of broken links appeared, so I went back to the working version. I'm not looking forward to repeating this process every few months....