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For some reason, many FileMaker developers think you can recover a file and continue using it. Well, you can if you want to live your life dangerously. Recover is a great tool when used properly. The proper use of the Recover feature is to recover a file and then import the recovered data into a backup of the file which is not damaged. In other words, the Recover feature is for recovering your data not your schema. Even with the new recovery features in FileMaker 10, always remember that FileMaker assumes you are recovering a file because you have no other choice. Therefore, the Recover feature will remove any suspect scripts, fields, layouts and other features it believes could be causing the problem. While the Recover feature could completely fix your file, it's also possible it may not remove all corruption even though the file appears to be functioning properly.
For more information on recovery, see the white paper titled "Demystifying FIleMaker Pro File Recovery" by Steven Blackwell, available in the Resources area of this web site.