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One week ago I experienced an odd and catastrophic failure of my MacBook Pro. The details of the failure are not important, and the relevant parts have been replaced, among them a new HDD. Side note: I've said it countless times - Apple Care is the only extended warranty worth having. My machine failed six days (!!!) before my three-year warranty expired. Not only did Apple replace everything quickly, but they increased my HDD from the stock 250 GB to 500 (I suspect that this was partially due to my complaint that the authorized repair center, not an Apple store, was marginally incompetent as they ignored the work order completely at first, and set about fixing something that wasn't problematic).

Here is my scenario: I use Carbon Copy Cloner to clone my MBP every other week, and Time Machine for the hourly backups. Several directories are excluded from TM, which include fairly standard exclusions (e.g., Trash, Downloads) and some non-standard ones (e.g., the applications folder, since I can easily restore these with either the clone, DVDs, or the App Store). When I got the MBP back, it had 10.5.8 installed, which is what was on the machine when I bought it (late 2008 model; the install discs for my MBP are in another city and state, which I can access in two weeks if needed). I used CCC to erase and clone to the new HDD, which went off without a hitch. My major concern is restoring the files from TM to the HDD, which are current to the machine's failure date (TM files are about two weeks newer than the clone).

I have scoured the help manuals for TM and CCC, but could not find an adequate, representative case such as mine. Now that the HDD has been cloned, do I need to use the Time Machine system restore procedure over the backup? I am concerned about whether or not it will overwrite the directories that conflict between the clone and the TM backups. Alternatively, should I boot from the clone and restore files from TM to it, then erase the internal HDD (again) to re-restore from the clone?

Ultimately, I am wondering whether it is safe to use a non-standard Time Machine backup to restore newer files over a clone. So, if a clone directory has five subdirectories, all but one of which are on the TM backup, will TM overwrite the parent directory and leave me with only those four subdirectories? Or, will TM leave the unique subdirectory alone and simply restore the other four that it contains?

Let me know if you have had this specific scenario or one very similar to it. I can leave things as-is and restore files as I find them missing, but I'd rather just get to the previous state. This should be totally possible, as these two backups (plus dropbox, forgot to mention) represent 100% of the machine's previous state.

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Unless software led to the demise of your previous drive, you have everything you need to restore your computer's state. Having restored from TM before, I see no problems using your TM backup. As always, make a clone before you restore, just in case. –  badams May 8 '12 at 15:52
    
Thank you for the comment. I already had/have a clone, though, and already restored from it. I am wondering whether it is safe to use a non-standard Time Machine backup to restore newer files over a clone. Basically, if a clone directory has five subdirectories, all but one of which are on the TM backup, will TM overwrite that and leave me with only those four subdirectories? Or, will TM leave the unique subdirectory alone and simply restore the other four that it contains? I will add this info to my question. –  soxman May 8 '12 at 16:00

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