How do I change the Quarantine directory that the Endpoint Agent uses when blocking files? Is there a way to change the time period that these files are kept in that directory?

If you configure the Endpoint Server under Server Detail you can set the 'File Recovery' location under the Agent Configuration tab.

The min setting to keep the files in this directory is 1 hour.

The max setting to keep the files in this directory is 999 hours which is 41.625000000033296 days.