Since everything still works & logs in OK, it looks like just ls
doesn't have permission to execute the folder and is showing the annoying ???
's.
Giving the folder a chmod +x
should fix it.
Here's some tests I did FYI:
$ mkdir test; touch test/1; touch test/2
$ ls -al test
total 0
drwxr-xr-x 2 user user 80 Dec 25 13:20 .
drwxrwxrwt 8 root root 300 Dec 25 13:20 ..
-rw-r--r-- 1 user user 0 Dec 25 13:20 1
-rw-r--r-- 1 user user 0 Dec 25 13:20 2
$ chmod -v -x test
mode of 'test' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
$ ls -al test
ls: cannot access 'test/.': Permission denied
ls: cannot access 'test/..': Permission denied
ls: cannot access 'test/2': Permission denied
ls: cannot access 'test/1': Permission denied
total 0
d????????? ? ? ? ? ? .
d????????? ? ? ? ? ? ..
-????????? ? ? ? ? ? 1
-????????? ? ? ? ? ? 2
$ chmod -v +x test
mode of 'test' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x)
$ ls -al test
total 0
drwxr-xr-x 2 user user 80 Dec 25 13:20 .
drwxrwxrwt 8 root root 300 Dec 25 13:20 ..
-rw-r--r-- 1 user user 0 Dec 25 13:20 1
-rw-r--r-- 1 user user 0 Dec 25 13:20 2
$ chmod -v -r test
mode of 'test' changed from 0755 (rwxr-xr-x) to 0311 (-wx--x--x)
$ ls -al test
ls: cannot open directory 'test': Permission denied