Hello,
We came across this exact issue in Query Studio after changing a few of the field names in the Framework Manager package. After logging a support ticket with Cognos, their response was that we needed to upgrade to Cognos 8.3. ( We're currently on 8.2). This bug is included on the list of fixes for 8.3. We replied stating that an upgrade was not a feasible option at the time, and Cognos eventually agreed to develop a patch to fix the issue in 8.2.
Upgrading to 8.3 fixes this issue, but if that's not an option I would contact Cognos support and explain the situation, and see if they can work with you to develop some kind of hotfix or patch that works in your environment.
Hope this helps,
Jay