It turns out my particular problem wasn't covered by other, similar cases, so I'm going to post my own answer describing the actual issue I had, and the solution I found to it.
In my case it appears that somehow my last "complete" Time Machine backup was in fact corrupted somehow; when I looked inside it I found that the contents of my user folder were missing, so Time Machine was in fact correct in thinking that it needed to backup everything from my user folder again.
To solve this I needed to delete the last "complete" backup on my Time Machine drive. To do this I opened my Time Machine volume in the Finder, and navigated inside the Backups.backupdb folder, my computer name and then found the folder with the most recent time and date. After taking a quick look at some of the largest folders I saw that my user folder (the biggest on my system) was empty.
To fix this problem I then ran the following command in Terminal:
sudo tmutil delete "/Volumes/Time Machine Backup/Backups.backupdb/MyComputer/2014-10-01-175432"
Of course you will need to replace the part in quotes with the correct path to the corrupted backup. You can also do this easily by instead typing sudo tmutil delete (with trailing space at the end) and then dragging the folder onto the Terminal window to have it add the path for you (it may include backslashes, this is normal). You'll need to run this command using an administrator account and enter its password, since only an administrator can alter Time Machine's backups.
For anyone experiencing a similar issue to what I was seeing, I would now highly recommend giving your latest backup a quick check to make sure that you aren't experiencing the same problem I was; although the chances of this corruption occurring seems extremely low (Time Machine would have to be forcibly interrupted or crash for it to occur, though having your Time Machine volume disconnect may do it), it doesn't take long to give your latest backup a quick check, but it can save you a lot of time before you go ahead and try other possible solutions.
If you aren't experiencing the same problem I did then I recommend trying the following links:
The best thing to do, to avoid major data loss, is to:
- copy personal files and folders from the TM disk image (they do not have symlinks, so no problem whatsoever). Obviously choose the latest backup.
- from the TM disk image write down on a piece of paper an entire list of all the apps in the Application folder and reinstall them from scratch (depending on what the app is, it might not be self-contained, therefore it might include some symlinks and/or preferences)
Even if you can successfully restore from the TM, you must reinstall from scratch utilities like
- Garageband/Logic additional instruments (if you have installed some)
- Java
- Adobe Flash Player/Shockwave Player
- Microsoft Silverlight
- XCode Command Line Tools
Best Answer
Yes - copying any of the folders will use the hard link to make a full copy of that moment in time. The hard links only work on the same filesystem, so you can test things if you are copying to the same volume but most instances where I do this, I'm copying to another volume (compressed disk image or physical/logical volume).
In a nutshell - using Finder (or rsync/ditto) to make a copy of any of the folders will result in a functional full copy of the system at that point in time with all the files intact.