Some commands can see a directory but not others?

There's a directory that had gone missing, I never intentionally deleted it (might've been accidental). Assume the directory structure is:

/parent  /dir    dirFile.js  parentFile.js

If I'm in /parent:

$ lsparentFile.js$ ls -a...parentFile.js$ mkdir dirmkdir: cannot create directory ‘dir’: File exists$ rm -rf dir<empty>$ ls dir<empty>$ stat dir  File: dir  Size: 4096            Blocks: 0          IO Block: 4096   directoryDevice: fh/15d  Inode: 1688849861548050  Links: 0Access: (0777/drwxrwxrwx)  Uid: ( 1000/       l)   Gid: ( 1000/       l)Access: 2020-07-14 16:35:37.808833200 -0400Modify: 2020-07-14 16:35:37.808833200 -0400Change: 2020-07-14 16:35:37.808833200 -0400 Birth: -

When this directory was last available, I modified dir/dirFile.js and ran git commit. Then, I noticed dir disappeared, so I ran git reset HEAD~1 --mixed. However, the file didn't come back and git status shows it was deleted.

I'm unable to git stash to undo the delete because it throws error: unable to create file dir/dirFile.js: No such file or directory.

I'm using Ubuntu 18.04.4 on WSL.

What's going on here?