Files missing from drive - and Time Machine (Freeway files)

A file that was just updated yesterday is now gone from the computer - everywhere. Gone from the internal drive and gone from time machine. When I do a search for the file type, the last update to it shows as December 19th. This is the day after I erase & installed Snow Leopard and brought the file back onto the machine from a backup drive. When I click "yesterday" in the sidebar, or "past week" it shows the application (Freeway) being used, but not the file.
Freeway is a little buggy with where it saves things, but all the resources for the file are still in the expected location. The .freeway itself, its backup on the internal hard drive, and its backup on Time Machine are all gone when I search in finder. This computer has been acting a little wonky, which is why I did the erase & install. Just last week a partition of the startup drive failed to mount. I turned off the computer, unplugged it for 30 seconds, and it was fine.
Is this a symptom of impending startup drive failure? Already repaired permissions and ran a repair disk on the drive where the files should have been.

It sounds like the files were deleted during the day yesterday.
If they were on your system when today's first Time Machine backup was done (ie, after midnight), they'll be on that backup. So if you haven't yet, look directly at today's first backup, via the "Star Wars" display. You may or may not have success searching the backup there, so be sure to check all the places you might have put them.
A very long shot is disk corruption, that somehow lost/overwrote the files. Verify your internal hd to be sure it's ok.

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I tried searching around on the new Apple discussion forum, but I find it much harder to use than the old forum I used to use.

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It is unlikely that you have regular churn on 2.75 TB of disk. I suggest identifying which drives and folders have the most activity and excluding those drives and directories that don't change much. It would be better to archive the data that doesn't change often and keep it out of Time Machine. Then you may be able to get away with a 2 TB Time Machine drive.

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John,
I'm not sure why you posted in the iMac forum so I'm going to attempt to get you to the correct spot. I would recommend reposting in the Time Machine Forum, this is part of the OS X forums (Leopard or Snow Leopard) because you are using Snow Leopard (your profile indicates you are) please click Apple Support Communities and type Snow Leopard. Then you can narrow the search down by clicking Refine this List.
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Here's Apple's public statement at http://www.apple.com/macosx/features/timemachine.html for what devices work with TM.
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Please follow these instructions:
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https://discussions.apple.com/thread/3258472

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http://pondini.org/OSX/Home.html
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Files missing from drive - and Time Machine (Freeway files)

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