How to access root apps folder again in Time Machine after a restore?

I just did a Time Machine full system restore which worked, but now it doesn't look like Time Machine is backing up my root level apps folder. All of my root apps were indeed restored, but if I try to go into Time Machine with my (root) Apps folder open, it switches the folder contents to my user apps instead so I don't have access to the root apps in TM. It doesn't appear to be backing them up at the root level anymore either (nothing in the exclusions that would cause this). Any ideas on what happened here? I have just one admin level account on this machine.

cubytus wrote:
Hi everyone,
I just reformated the MacBook hard drive using Extended HFS+, journaled partition to get rid of the case-sensitiveness, which is incompatible with just ONE of my softwares. As such, TM partition is formatted as Extended HFS+, journaled and case-sensitive.
This mis-match is likely to cause trouble in the future. If you have, for example, two files named "FileA" and "filea" in the same folder on the TM drive, and try to restore them to your case-ignorant HD, TM is going to have a problem. I've never tried it, so I can't tell you whether it will overlay the first one it restores with the second, or crash, or what, but it can't be done.
And you may have some of these without realizing it -- if you ever changed a capital to lower-case, or vice-versa, after a file's initial backup, it's a possibility.
Indeed, I checked directly in the Time Machine tree on the external hard drive with Apple+I keys, and 'cubytus' was not listed in the permissions.
No, TM automatically denies everything to everybody, among other things, in it's backups, to keep us mere mortals from messing with them. The original file permissions are kept separately, and TM should restore them along with the files, as they were.
What you're probably seeing is, the user that you're signed-on as won't have those permissions, once TM restores the files. I'd suggest trying the same procedure as your other, or original user -- see if you get the same message.

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