I experienced this before.
That time the qvw was not so big, but apparently I had problems with shared and meta files.
So if you move those files to another folder (or delete them) the server will just recreate fresh files.
In my case, it fixed the problem.
It was a long time ago. Now, I also suggest you try to run QlikView Power Tool on those .shared and .meta files to check if they are ok.
Maybe a defrag will help ( from Power Tools)
Please, report your result.
I agree with Erich, it sounds like a problem with the .shared file. DO NOT defrag it however, as that has been known to cause even more problems.
What you should do is open the .shared file with the Shared File Viewer and simply resave it. It will make a backup for you and if you reload it most of the pink/red coloring should be gone. You might have to save it a second time.
Absolutely do not defrag it.