Did you try opening the QVW files with QlikView Desktop 11 and reloading and saving them? In case this does not work, backup the QlikView documents file and remove in the Server's folder the .PGO, .Shared and .Meta files. You may lose some information, but you always be able to go back restoring the old folder.
Is that happening in the latest release of QlikView 11 SR1 (11282) ?
I had the same issue. Support was able to help, sorta - he found that we could save metadata in another folder on another drive, and then copy the resulting .meta file back to where it belongs. He was not able to offer any ideas as to why this started happening (after upgrading from 10 to 11), why it affected only some files, or why it could save meta in one folder but not another (in both folders, the QlikView service has full privs).
If QlikView used an open format such as XML, rather than this proprietary binary format, we could work around bugs like this by hand-editing the files. We could also write our own batch editors. Imagine being able to adjust the settings for all 75 files at once instead of tediously click-click-click-clicking through the QMS! I would weep for joy.