We used Migration Manager for SharePoint and Notes Migrator to migrate Notes DB to SharePoint.
The issue is in Notes Migration. The tool uses QuestLinkTracking Database to keep track of notes link inside each discussion items and it is using Questlink.aspx page to redirect to proper item.
If the redirection still working that means you have quest.nmsp.frontend.wsp solution installed in your SharePoint. It performs the redirection.
There are the following options available:
1. Perform upgrade of SharePoint. On SharePoint 2010 install the NMSP services. (quest.nmsp.frontend.wsp and quest.nmsp.frontend.wsp solutions). Configure Link Tracking on SharePoint 2010 to use the old Link tracking database. With these solutions, the redirection will work the same way it worked on SharePoint 2007.
If you remember the version of NMSP used on source, you may install the same version on target... or install the latest version.. but in this case, backup the Link Tracking database before configuring the service.
2. Finalize links. The links can be finalized before upgrading.
From User Guide:
You can use this tool to update or permanently replace all Dynamic Links in a set of migrated documents. This works for links in SharePoint List Items, SharePoint Pages, InfoPath documents, Word documents or any other SharePoint target you chose to migrate to.
You can use this tool when updating the Link Tracking Database is not enough and you want to update the actual Dynamic Links in the migrated documents. The most common reason to do this is to permanently replace all Dynamic Links with direct links to the last known locations of the target documents. A secondary reason might be to change the location of your Redirector Page.
Links can be finalized from Console of Admin pages in Central Administration (existence of these pages depend on version of NMSP).
Please refer to Notes Migrator User Guide for more details about Link Finalization.