There are a few different reasons why you might need to manually cache a file on a BigFix Root Server.
One of them is that the file being downloaded in a prefetch is not available on the public internet directly. The most common case is where a login is required in order to obtain the file. This is most common with certain versions of Oracle JAVA.
Another case is when only the latest version of the software is available from the vendor to download directly, but the version referenced in the prefetch is no longer available. This is most common with Google Chrome.
In any case where the download is not available, you can put the binary in the right place on the root server to solve this issue.
C:\Program Files (x86)\BigFix Enterprise\BES Server\wwwrootbes\bfmirror\downloads\sha1