When a ISE 9.2.04i or older Project Navigator project is opened in ISE 10.1, a dialog box appears indicating that the project needs to be migrated to the ISE 10.1 version. The dialog box also states that the existing project will be archived to a file named <project name>_ise10migration.zip. Upon clicking OK, the archive and migration are successful. However, it appears that the <project>.ise file inside the <project name>_ise10migration.zip has a new timestamp and size.
During migration, the .ise file saved in the <project name>_ise10migration.zip is incorrectly touched. From preliminary testing, it appears that the .ise project file is still a valid project for the ISE version used before the migration and functionally equivalent to the old project.
Xilinx is investigating the exact cause of the .ise file change with the intent to fix this in a coming service pack.
The <project>.ise_backup file is not touched in the <project name>_ise10migration.zip archive or in the migrated project. If you want to be certain that the project file is exactly equivalent, you can rename this file <project>.ise.