You might want to post a couple of lines from your csv file. For example, is it of the form
item1,"item with comma, in name",item3.
You can get a list of the directories under the parent directory using the find command:
find /path/to/parent/directory -type f
Given the large number of entries, it may work best if you can process the csv file and produce a file of directories. (Let's call it csvdirs for illustration sake.)
Then you could use:
grep -f csv-dirs current-dir-list
to find matches. A better way would be to sort both lists and use the "comm" command.
comm compares to sorted lists and outputs three columns.
First column: lines unique to file1; Second column: lines unique to file2; Third column: lines common to both files. You can turn off any of the columns with the -1, -2, and -3 options.
To list common entries, use "comm -12 file1 file2".