Hi there!Read my DISCLAIMER at the end of this message before you elect to follow my suggestions below. Before following any person's suggestions, you should exercise ordinary prudence and care. By following my suggestions, you agree to hold me harmless and you agree to my DISCLAIMER. If not, do not follow my suggestions, but call Finale Technical Support.
Backup your back up file to a floppy if it fits, or to some other off-line storage. Or, create an account on https://www.xdrive.com, and store it there. In other words, protect your only backup.
At the finder level, make a duplicate of your backup file that contains all the correct notes and markings. Place that duplicate file in a unique place of your choosing within the finale directory tree (avoiding name collisions, etc.)
Now, click once on the Finale 2000 program icon. Then in the file menu, select "Get Information". A popup window will display information about the Finale Application. On the lower right, you will find two memory values. Make them both at least 10,000K.
Then, start Finale, and open your duplicate of the backup, and make a change, assuming all is well, then save the change to the file, then, make the next change, assuming all is well, then save the change to the file, etc. Now, when you get to the point where the problem occurred, backup your changed file to off-line storage, restart Finale, and run the Make Fit command, then inspect the music. If all is well, save your changes, and you're done. If, not, close the file, forget changes (click Don't save), quit Finale, File Menu -->get information, and modify the memory to a higher value, restart Finale, re-open the file to the last state it was in before the Make Fit command. Run the Make Fit command again, and see if it works now.
If none of this works, perhaps Finale is re-baring the music due to some time signature change. However, it is not likely that you changed the time signature, during your changes. It really sounds to me like it is a memory problem, due to the way Finale is setup with its factory settings of memory sllocation. Another solution may be to drag your Finale preferences file to the trash. This will cause you to lose your registration information, but just enter your Finale serial number and name and you'll be back in business (You may have to insert your Finale 2000 CDROM during that process)
I hope I was of some help to you.
DISCLAIMER
Any use of the above suggestions by me is totally at your own risk and I disclaim any responsibility, and/or liability for any data loss, system crashes, or other harm that may result from your following my suggestions.