Edit: https://wiki.covecube.com/StableBit_DrivePool_Q5510455 is the normal, Stablebit-approved method to reset NTFS permissions. It should suffice in most cases, and it's easier to do than my method, so try it first.
To fix broken NTFS permissions I now use a freeware program called SetACL because - at least in my experience - it properly supports both long paths and unicode and can fix damaged security records that Windows builtin tab and utilities like takeown and icacls can’t (for reasons that personally I boil down to “unicode and long paths were added to Windows partly via the programming equivalent of lots of duct tape”). If you're a sysadmin I recommend checking out the rest of the site too!
The following is a quick guide to how I use SetACL to reset my pool permissions on my own machines. Your mileage may vary; you should always have backups of anything you don't want to lose.
Note: if you have customised your pool's security permissions (e.g. for multiple users with different access rights) be aware that you may need to customise the following commands (particularly the fourth) in this post to suit your changes, or adjust the permissions subsequently.
I download the SetACL for Administrators (not the Studio) from here. It's freeware (as is the Studio version if you want a GUI). Open the zip file and copy SetACL.exe from the 32bit or 64bit folder (as appropriate) to wherever you want to keep it so long as that location is OUTSIDE of your pools.
Open a command prompt as an Administrator and enter the following commands in order (where X:\ is the location of SetACL.exe and P:\ is the location of your pool drive - and that's very important, do not get confused, do not put in the wrong drive letters):
Net stop "stablebit drivepool service"
X:\SetACL.exe -on P:\ -ot file -actn setowner -ownr "n:Administrators" -rec cont_obj -fltr "System Volume Information" -fltr "$RECYCLE.BIN"
X:\SetACL.exe -on P:\ -ot file -actn clear -clr "dacl,sacl" -actn rstchldrn -rst "dacl,sacl" -fltr "System Volume Information" -fltr "$RECYCLE.BIN"
X:\SetACL.exe -on P:\ -ot file -actn ace -ace "n:Authenticated Users;p:change" -ace "n:SYSTEM;p:full" -ace "n:Administrators;p:full" -ace "n:Users;p:read_ex" -fltr "System Volume Information" -fltr "$RECYCLE.BIN"
Net start "stablebit drivepool service"
The first and last commands stop and start DrivePool respectively; the second command takes ownership (since you need to have ownership before you can alter any permissions that would otherwise prevent you from altering permissions), the third resets all existing permissions and enables inheritance of new permissions, and the fourth grants new permissions (I’ve used the Windows 10 defaults that should be compatible with all versions of Windows that are compatible with DrivePool); the special folders used for System Volume Information and Recycle Bin have been excluded as a precaution.
If you are still getting permission errors even after running all five commands in order, you can try running them directly on the individual poolpart folders. So for example if "E:" was one of the drives you'd added to the pool, you'd use E:\PoolPart.guidstring instead of P:\ in the above commands (tip: when you're using the command prompt, pressing the tab key after you've typed PoolPart into the command prompt should fill in the correct guidstring for you). Note: poolpart folders contain a ".covefs" folder; do not apply non-default permissions to that folder unless you know exactly what you are doing.
If your pool contains a lot of files (the size of each file doesn't matter), these commands may take a while to complete (my primary pool, with ~600k files, takes a couple of hours).