Roaming Raid Upgrade, lost access to some shares

I moved my 6tb drives from my EX2 Nas to my shinny new PR4100, and plan to add 2 more 6TB in the future and convert to raid 5. however a few of my folders I have lost access to and cannot change the permissions they are grayed out, I assume there is a way to do this via SSH but not sure the commands any help would be great

You probably have to fix the owner of the files, not the permissions.
But with the permissions it is a bit easier.

SSH into the box.
Go to your shares directory and show the contents.

root@MyCloudPR4100 # cd /shares
root@MyCloudPR4100 # ls
someshare   someothershare   awesomeshare    Volume_1 --> do not touch this!
root@MyCloudPR4100 # cd someshare

Easy fix but not that good
Fix permissions of files in current path

find . -type f -print0 | xargs -0 chmod 666

Fix permissions of directories in current path

find . -type d -print0 | xargs -0 chmod 777

Better fix
Get your user ID and group by creating a test file somewhere

ls -l /path/to/testfile

You see it is owned by user 1002 and group 2002 (or similar numbers).

find . -print0 | xargs -0 chown 1002:2002
find . -type f -print0 | xargs -0 chmod 644
find . -type d -print0 | xargs -0 chmod 755

See also