Ohh, blue. I personally refer to it as filled.
Checked means all files are read-only. Unchecked means no files are read-only. Filled (blue) means some (anywhere from one to almost every file) is read-only.
The filled box only applies to folders containing files (or subfolders).
I'm sure you're fine now. All files in which you could remove the read-only attribute from are likely changed and can be modified further without issue.